Execution of AUVprocess_main version 1.86 at 2018-05-25T16:58:11Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2014, ['290.00'], '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: 2014.290.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/ 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/2014/2014290/2014.290.00/navigation.nc') Creating vector time with 96110 elements. Creating vector mPos_x with 96110 elements. Creating vector time with 96110 elements. Creating vector mPos_y with 96110 elements. Creating vector time with 96110 elements. Creating vector mDepth with 96110 elements. Creating vector time with 96110 elements. Creating vector mGpsNorth with 96110 elements. Creating vector time with 96110 elements. Creating vector mGpsEast with 96110 elements. Creating vector time with 96110 elements. Creating vector mGpsValid with 96110 elements. Creating vector time with 96110 elements. Creating vector mPhi with 96110 elements. Creating vector time with 96110 elements. Creating vector mTheta with 96110 elements. Creating vector time with 96110 elements. Creating vector mPsi with 96110 elements. Creating vector time with 96110 elements. Creating vector mOmega_x with 96110 elements. Creating vector time with 96110 elements. Creating vector mOmega_y with 96110 elements. Creating vector time with 96110 elements. Creating vector mOmega_z with 96110 elements. Creating vector time with 96110 elements. Creating vector mPsaRange with 96110 elements. Creating vector time with 96110 elements. Creating vector mAltitude with 96110 elements. Creating vector time with 96110 elements. Creating vector multibeamAltitude with 96110 elements. Creating vector time with 96110 elements. Creating vector mDvlAltitude with 96110 elements. Creating vector time with 96110 elements. Creating vector mEchoAltitude with 96110 elements. Creating vector time with 96110 elements. Creating vector mEchoHorizRange with 96110 elements. Creating vector time with 96110 elements. Creating vector mEchoAltitudeLast with 96110 elements. Creating vector time with 96110 elements. Creating vector mEchoHorizRangeLast with 96110 elements. Creating vector time with 96110 elements. Creating vector mEchoNumOfPings with 96110 elements. Creating vector time with 96110 elements. Creating vector nadirCnts with 96110 elements. Creating vector time with 96110 elements. Creating vector obstacleCnts with 96110 elements. Creating vector time with 96110 elements. Creating vector mWaterSpeed with 96110 elements. Creating vector time with 96110 elements. Creating vector mDvlValid with 96110 elements. Creating vector time with 96110 elements. Creating vector mDvlNewData with 96110 elements. Creating vector time with 96110 elements. Creating vector mDeltaT with 96110 elements. Creating vector time with 96110 elements. Creating vector nfix with 96110 elements. Creating vector time with 96110 elements. Creating vector efix with 96110 elements. Creating vector time with 96110 elements. Creating vector filter_north with 96110 elements. Creating vector time with 96110 elements. Creating vector filter_east with 96110 elements. Creating vector time with 96110 elements. Creating vector filter_depth with 96110 elements. Creating vector time with 96110 elements. Creating vector north_current with 96110 elements. Creating vector time with 96110 elements. Creating vector east_current with 96110 elements. Creating vector time with 96110 elements. Creating vector speed_bias with 96110 elements. Creating vector time with 96110 elements. Creating vector heading_bias with 96110 elements. Creating vector time with 96110 elements. Creating vector latitude with 96110 elements. Creating vector time with 96110 elements. Creating vector longitude with 96110 elements. Creating vector time with 96110 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/navigation.nc'); processNav(): median of positive valued depths = 14.7337 processNav(): Finding depths less than 103.1362 and times > 0 processNav(): length(Nav.depth) = 96110 processNav(): length(gindx) = 96110 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/2014/2014290/2014.290.00/gps.nc') Creating vector time with 2406 elements. Creating vector hours with 2406 elements. Creating vector time with 2406 elements. Creating vector minutes with 2406 elements. Creating vector time with 2406 elements. Creating vector seconds with 2406 elements. Creating vector time with 2406 elements. Creating vector centiSeconds with 2406 elements. Creating vector time with 2406 elements. Creating vector latitude with 2406 elements. Creating vector time with 2406 elements. Creating vector longitude with 2406 elements. Creating vector time with 2406 elements. Creating vector quality with 2406 elements. Creating vector time with 2406 elements. Creating vector numberOfSatellites with 2406 elements. Creating vector time with 2406 elements. Creating vector hdop with 2406 elements. Creating vector time with 2406 elements. Creating vector antennaHeight with 2406 elements. Creating vector time with 2406 elements. Creating vector geoHeight with 2406 elements. Creating vector time with 2406 elements. Creating vector dgpsDataAge with 2406 elements. Creating vector time with 2406 elements. Creating vector dgpsRSID with 2406 elements. Creating vector time with 2406 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/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/2014/2014290/2014.290.00/parosci.nc') Creating vector time with 189382 elements. Creating vector depth with 189382 elements. Creating vector time with 189382 elements. Creating vector temp with 189382 elements. Creating vector time with 189382 elements. Creating vector pressure with 189382 elements. Creating vector time with 189382 elements. Creating vector temp_period with 189382 elements. Creating vector time with 189382 elements. Creating vector pres_period with 189382 elements. Creating vector time with 189382 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.17025 max(Depth.data) = 82.9612 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.17025 max(Depth.data) = 82.9612 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/2014/2014290/2014.290.00/hydroscatlog.nc') Creating vector time with 76997 elements. Creating vector Seconds with 76997 elements. Creating vector time with 76997 elements. Creating vector HundrethsOfSeconds with 76997 elements. Creating vector time with 76997 elements. Creating vector Snorm1 with 76997 elements. Creating vector time with 76997 elements. Creating vector Snorm2 with 76997 elements. Creating vector time with 76997 elements. Creating vector Snorm3 with 76997 elements. Creating vector time with 76997 elements. Creating vector Gain_Status_1 with 76997 elements. Creating vector time with 76997 elements. Creating vector Gain_Status_2 with 76997 elements. Creating vector time with 76997 elements. Creating vector Gain_Status_3 with 76997 elements. Creating vector time with 76997 elements. Creating vector RawDepthValue with 76997 elements. Creating vector time with 76997 elements. Creating vector RawTempValue with 76997 elements. Creating vector time with 76997 elements. Creating vector Temperature with 76997 elements. Creating vector time with 76997 elements. Creating vector ErrorValue with 76997 elements. Creating vector time with 76997 elements. Creating vector bb470 with 76997 elements. Creating vector time with 76997 elements. Creating vector bb676 with 76997 elements. Creating vector time with 76997 elements. Creating vector fl676u with 76997 elements. Creating vector time with 76997 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/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/2014/2014290/2014.290.00/ctdDriver.nc') Creating vector time with 76969 elements. Creating vector conductivity with 76969 elements. Creating vector time with 76969 elements. Creating vector temperature with 76969 elements. Creating vector time with 76969 elements. Creating vector cond_frequency with 76969 elements. Creating vector time with 76969 elements. Creating vector temp_frequency with 76969 elements. Creating vector time with 76969 elements. Creating vector spare with 76969 elements. Creating vector time with 76969 elements. Creating vector humidity with 76969 elements. Creating vector time with 76969 elements. Creating vector flow1 with 76969 elements. Creating vector time with 76969 elements. Creating vector CDOM with 76969 elements. Creating vector time with 76969 elements. Creating vector dissolvedO2 with 76969 elements. Creating vector time with 76969 elements. Creating vector salinity with 76969 elements. Creating vector time with 76969 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/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/2014/2014290/2014.290.00/ctdDriver2.nc') Creating vector time with 76968 elements. Creating vector conductivity with 76968 elements. Creating vector time with 76968 elements. Creating vector temperature with 76968 elements. Creating vector time with 76968 elements. Creating vector cond_frequency with 76968 elements. Creating vector time with 76968 elements. Creating vector temp_frequency with 76968 elements. Creating vector time with 76968 elements. Creating vector flow2 with 76968 elements. Creating vector time with 76968 elements. Creating vector spare with 76968 elements. Creating vector time with 76968 elements. Creating vector salinity with 76968 elements. Creating vector time with 76968 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/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/2014/2014290/2014.290.00/isuslog.nc') Creating vector time with 14918 elements. Creating vector isusNitrate with 14918 elements. Creating vector time with 14918 elements. Creating vector isusTemp with 14918 elements. Creating vector time with 14918 elements. Creating vector isusQuality with 14918 elements. Creating vector time with 14918 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/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/2014/2014290/2014.290.00/biolume.nc') Creating vector time with 18948 elements. Creating vector rrr with 18948 elements. Creating vector time with 18948 elements. Creating vector cal_striing with 18948 elements. Creating vector time with 18948 elements. Creating vector avg_biolume with 18948 elements. Creating vector time with 18948 elements. Creating vector pump with 18948 elements. Creating vector time with 18948 elements. Creating vector system_voltage with 18948 elements. Creating vector time with 18948 elements. Creating vector flow with 18948 elements. Creating vector time with 18948 elements. Creating vector HV with 18948 elements. Creating vector time with 18948 elements. Creating vector reserved with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_0 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_1 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_2 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_3 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_4 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_5 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_6 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_7 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_8 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_9 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_10 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_11 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_12 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_13 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_14 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_15 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_16 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_17 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_18 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_19 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_20 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_21 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_22 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_23 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_24 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_25 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_26 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_27 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_28 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_29 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_30 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_31 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_32 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_33 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_34 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_35 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_36 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_37 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_38 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_39 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_40 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_41 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_42 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_43 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_44 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_45 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_46 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_47 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_48 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_49 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_50 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_51 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_52 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_53 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_54 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_55 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_56 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_57 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_58 with 18948 elements. Creating vector time with 18948 elements. Creating vector raw_59 with 18948 elements. Creating vector time with 18948 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/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/2014/2014290/2014.290.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (1834 x 994) with 1822996 elements. Creating vector time with 1834 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (1834 x 994) with 1822996 elements. Creating vector time with 1834 elements. Creating vector bin with 994 elements. Creating matrix countList (1834 x 994) with 1822996 elements. Creating vector time with 1834 elements. Creating vector bin with 994 elements. Creating vector LCcount with 1834 elements. Creating vector time with 1834 elements. Creating vector transCount with 1834 elements. Creating vector time with 1834 elements. Creating vector nonTransCount with 1834 elements. Creating vector time with 1834 elements. Creating vector ai_mean with 1834 elements. Creating vector time with 1834 elements. Creating vector ai_min with 1834 elements. Creating vector time with 1834 elements. Creating vector ai_max with 1834 elements. Creating vector time with 1834 elements. Creating vector ai_std with 1834 elements. Creating vector time with 1834 elements. Creating vector esd_mean with 1834 elements. Creating vector time with 1834 elements. Creating vector esd_min with 1834 elements. Creating vector time with 1834 elements. Creating vector esd_max with 1834 elements. Creating vector time with 1834 elements. Creating vector esd_std with 1834 elements. Creating vector time with 1834 elements. Creating vector countSum with 1834 elements. Creating vector time with 1834 elements. Creating vector snapshot with 1834 elements. Creating vector time with 1834 elements. Creating vector threshold with 1834 elements. Creating vector time with 1834 elements. Creating vector sampleCount with 1834 elements. Creating vector time with 1834 elements. Creating vector flowCount with 1834 elements. Creating vector time with 1834 elements. Creating vector flowTime with 1834 elements. Creating vector time with 1834 elements. Creating vector bufferStatus with 1834 elements. Creating vector time with 1834 elements. Creating vector laserLevel with 1834 elements. Creating vector time with 1834 elements. Creating vector counter with 1834 elements. Creating vector time with 1834 elements. Creating vector counterPeriod with 1834 elements. Creating vector time with 1834 elements. Creating vector laserControl with 1834 elements. Creating vector time with 1834 elements. Creating vector countUnknownFrameCharacter with 1834 elements. Creating vector time with 1834 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 1834 elements. Creating vector time with 1834 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 1834 elements. Creating vector time with 1834 elements. Creating vector flowSpeed with 1834 elements. Creating vector time with 1834 elements. Creating vector countShortLFrameError with 1834 elements. Creating vector time with 1834 elements. Creating vector countGarbledLFrame with 1834 elements. Creating vector time with 1834 elements. Creating vector cFrameEsecs with 1834 elements. Creating vector time with 1834 elements. Creating vector correctedSampleCountList with 1834 elements. Creating vector time with 1834 elements. Creating vector time with 1834 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014290/2014.290.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.290.00.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_2014.290.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 10 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_290_00_290_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_290_00_290_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_290_00_290_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 = 260 Gridding with nix = 780, iZ = 163 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 92248 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 92248 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: 10/17/2014 06:30 to 10/17/2014 13:29 swr = 0.7106 22.3162 135.2731 208.9739 405.7532 681.5959 617.6187 376.6766 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_290_00_290_00_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/2014290_GulperTimes.txt && touch ../results/2014290_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/2014/2014290/2014.290.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2014/2014290/2014.290.00/syslog -startEsecs 1413560278.7698 -surveyName Dorado389_2014_290_00_290_00 >> ../results/2014290_GulperTimes.txt Executing: removeGulpDups.py ../results/2014290_GulperTimes.txt Bottle: 0 Time: 1413561291.67 Depth: 2.112 Dist: 1.1842 Bottle: 1 Time: 1413561669.86 Depth: 3.1962 Dist: 1.6931 Bottle: 2 Time: 1413561992.07 Depth: 3.7304 Dist: 2.1362 Bottle: 3 Time: 1413562309.07 Depth: 4.5515 Dist: 2.598 Bottle: 4 Time: 1413562655.67 Depth: 3.505 Dist: 3.1109 Bottle: 5 Time: 1413564628.67 Depth: 12.2224 Dist: 5.9092 Bottle: 6 Time: 1413565257.47 Depth: 25.3572 Dist: 6.8255 Bottle: 7 Time: 1413565888.47 Depth: 18.2985 Dist: 7.771 Bottle: 8 Time: 1413566964.07 Depth: 25.0177 Dist: 9.2225 Bottle: 9 Time: 1413567305.47 Depth: 26.1981 Dist: 9.6668 Bottle: 10 Time: 1413567609.27 Depth: 22.9557 Dist: 10.0699 Bottle: 11 Time: 1413567917.87 Depth: 21.7455 Dist: 10.474 Bottle: 12 Time: 1413573932.26 Depth: 22.7631 Dist: 18.2371 Bottle: 13 Time: 1413574240.26 Depth: 14.7452 Dist: 18.7025 Bottle: 14 Time: 1413574904.27 Depth: 1.6662 Dist: 19.5787 Bottle: 15 Time: 1413575429.07 Depth: 6.6951 Dist: 20.3017 Bottle: 16 Time: 1413576405.07 Depth: 5.0956 Dist: 21.5805 Bottle: 17 Time: 1413576784.47 Depth: 7.5907 Dist: 22.0972 Bottle: 18 Time: 1413577389.87 Depth: 7.3971 Dist: 22.9442 Bottle: 19 Time: 1413577796.27 Depth: 3.3601 Dist: 23.4827 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_290_00_290_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_2014_290_00_290_00_2column.png Elapsed time to save image: 10 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_290_00_290_00_biolume.png Elapsed time to save image: 37 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_290_00_290_00_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_290_00_290_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_290_00_290_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_290_00_290_00_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_290_00_290_00_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_290_00_290_00_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_290_00_290_00_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_290_00_290_00_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_290_00_290_00_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_290_00_290_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_290_00_290_00_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_290_00_290_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_290_00_290_00_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_290_00_290_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_290_00_290_00_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_290_00_290_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_290_00_290_00_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_290_00_290_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_290_00_290_00_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_290_00_290_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_290_00_290_00_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_290_00_290_00_Chlorophyll_Fluorescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_290_00_290_00_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_290_00_290_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_290_00_290_00_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_290_00_290_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_290_00_290_00_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_290_00_290_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_290_00_290_00.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_290_00_290_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_2014_290_00_290_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 602 NaN values in array of lon that is 14918 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 14316 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 14316 are not equal to number of Lat lon points = 14918 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_290_00_290_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_290_00_290_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_290_00_290_00.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_290_00_290_00_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... 1 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_2014_290_00_290_00_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_290_00_290_00.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_290_00_290_00_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_290_00_290_00.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_290_00_290_00 processed" mccann@mbari.org < mail_Dorado389_2014_290_00_290_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.290.00.mat Processing time: 158 seconds