Execution of AUVprocess_main version 1.86 at 2018-05-24T22:10:13Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2014, ['211.03'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd2') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2014.211.03 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/ 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/2014/2014211/2014.211.03/navigation.nc') Creating vector time with 54464 elements. Creating vector mPos_x with 54464 elements. Creating vector time with 54464 elements. Creating vector mPos_y with 54464 elements. Creating vector time with 54464 elements. Creating vector mDepth with 54464 elements. Creating vector time with 54464 elements. Creating vector mGpsNorth with 54464 elements. Creating vector time with 54464 elements. Creating vector mGpsEast with 54464 elements. Creating vector time with 54464 elements. Creating vector mGpsValid with 54464 elements. Creating vector time with 54464 elements. Creating vector mPhi with 54464 elements. Creating vector time with 54464 elements. Creating vector mTheta with 54464 elements. Creating vector time with 54464 elements. Creating vector mPsi with 54464 elements. Creating vector time with 54464 elements. Creating vector mOmega_x with 54464 elements. Creating vector time with 54464 elements. Creating vector mOmega_y with 54464 elements. Creating vector time with 54464 elements. Creating vector mOmega_z with 54464 elements. Creating vector time with 54464 elements. Creating vector mPsaRange with 54464 elements. Creating vector time with 54464 elements. Creating vector mAltitude with 54464 elements. Creating vector time with 54464 elements. Creating vector multibeamAltitude with 54464 elements. Creating vector time with 54464 elements. Creating vector mDvlAltitude with 54464 elements. Creating vector time with 54464 elements. Creating vector mEchoAltitude with 54464 elements. Creating vector time with 54464 elements. Creating vector mEchoHorizRange with 54464 elements. Creating vector time with 54464 elements. Creating vector mEchoAltitudeLast with 54464 elements. Creating vector time with 54464 elements. Creating vector mEchoHorizRangeLast with 54464 elements. Creating vector time with 54464 elements. Creating vector mEchoNumOfPings with 54464 elements. Creating vector time with 54464 elements. Creating vector nadirCnts with 54464 elements. Creating vector time with 54464 elements. Creating vector obstacleCnts with 54464 elements. Creating vector time with 54464 elements. Creating vector mWaterSpeed with 54464 elements. Creating vector time with 54464 elements. Creating vector mDvlValid with 54464 elements. Creating vector time with 54464 elements. Creating vector mDvlNewData with 54464 elements. Creating vector time with 54464 elements. Creating vector mDeltaT with 54464 elements. Creating vector time with 54464 elements. Creating vector nfix with 54464 elements. Creating vector time with 54464 elements. Creating vector efix with 54464 elements. Creating vector time with 54464 elements. Creating vector filter_north with 54464 elements. Creating vector time with 54464 elements. Creating vector filter_east with 54464 elements. Creating vector time with 54464 elements. Creating vector filter_depth with 54464 elements. Creating vector time with 54464 elements. Creating vector north_current with 54464 elements. Creating vector time with 54464 elements. Creating vector east_current with 54464 elements. Creating vector time with 54464 elements. Creating vector speed_bias with 54464 elements. Creating vector time with 54464 elements. Creating vector heading_bias with 54464 elements. Creating vector time with 54464 elements. Creating vector latitude with 54464 elements. Creating vector time with 54464 elements. Creating vector longitude with 54464 elements. Creating vector time with 54464 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/navigation.nc'); processNav(): median of positive valued depths = 20.4649 processNav(): Finding depths less than 143.2542 and times > 0 processNav(): length(Nav.depth) = 54464 processNav(): length(gindx) = 54464 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/2014/2014211/2014.211.03/gps.nc') Creating vector time with 608 elements. Creating vector hours with 608 elements. Creating vector time with 608 elements. Creating vector minutes with 608 elements. Creating vector time with 608 elements. Creating vector seconds with 608 elements. Creating vector time with 608 elements. Creating vector centiSeconds with 608 elements. Creating vector time with 608 elements. Creating vector latitude with 608 elements. Creating vector time with 608 elements. Creating vector longitude with 608 elements. Creating vector time with 608 elements. Creating vector quality with 608 elements. Creating vector time with 608 elements. Creating vector numberOfSatellites with 608 elements. Creating vector time with 608 elements. Creating vector hdop with 608 elements. Creating vector time with 608 elements. Creating vector antennaHeight with 608 elements. Creating vector time with 608 elements. Creating vector geoHeight with 608 elements. Creating vector time with 608 elements. Creating vector dgpsDataAge with 608 elements. Creating vector time with 608 elements. Creating vector dgpsRSID with 608 elements. Creating vector time with 608 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/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/2014/2014211/2014.211.03/parosci.nc') Creating vector time with 107417 elements. Creating vector depth with 107417 elements. Creating vector time with 107417 elements. Creating vector temp with 107417 elements. Creating vector time with 107417 elements. Creating vector pressure with 107417 elements. Creating vector time with 107417 elements. Creating vector temp_period with 107417 elements. Creating vector time with 107417 elements. Creating vector pres_period with 107417 elements. Creating vector time with 107417 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.2783 max(Depth.data) = 67.4744 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.2783 max(Depth.data) = 67.4744 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/2014/2014211/2014.211.03/hydroscatlog.nc') Creating vector time with 43697 elements. Creating vector Seconds with 43697 elements. Creating vector time with 43697 elements. Creating vector HundrethsOfSeconds with 43697 elements. Creating vector time with 43697 elements. Creating vector Snorm1 with 43697 elements. Creating vector time with 43697 elements. Creating vector Snorm2 with 43697 elements. Creating vector time with 43697 elements. Creating vector Snorm3 with 43697 elements. Creating vector time with 43697 elements. Creating vector Gain_Status_1 with 43697 elements. Creating vector time with 43697 elements. Creating vector Gain_Status_2 with 43697 elements. Creating vector time with 43697 elements. Creating vector Gain_Status_3 with 43697 elements. Creating vector time with 43697 elements. Creating vector RawDepthValue with 43697 elements. Creating vector time with 43697 elements. Creating vector RawTempValue with 43697 elements. Creating vector time with 43697 elements. Creating vector Temperature with 43697 elements. Creating vector time with 43697 elements. Creating vector ErrorValue with 43697 elements. Creating vector time with 43697 elements. Creating vector bb470 with 43697 elements. Creating vector time with 43697 elements. Creating vector bb676 with 43697 elements. Creating vector time with 43697 elements. Creating vector fl676u with 43697 elements. Creating vector time with 43697 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/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/2014/2014211/2014.211.03/ctdDriver.nc') Creating vector time with 43648 elements. Creating vector conductivity with 43648 elements. Creating vector time with 43648 elements. Creating vector temperature with 43648 elements. Creating vector time with 43648 elements. Creating vector cond_frequency with 43648 elements. Creating vector time with 43648 elements. Creating vector temp_frequency with 43648 elements. Creating vector time with 43648 elements. Creating vector spare with 43648 elements. Creating vector time with 43648 elements. Creating vector humidity with 43648 elements. Creating vector time with 43648 elements. Creating vector flow1 with 43648 elements. Creating vector time with 43648 elements. Creating vector CDOM with 43648 elements. Creating vector time with 43648 elements. Creating vector dissolvedO2 with 43648 elements. Creating vector time with 43648 elements. Creating vector salinity with 43648 elements. Creating vector time with 43648 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/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/2014/2014211/2014.211.03/ctdDriver2.nc') Creating vector time with 43645 elements. Creating vector conductivity with 43645 elements. Creating vector time with 43645 elements. Creating vector temperature with 43645 elements. Creating vector time with 43645 elements. Creating vector cond_frequency with 43645 elements. Creating vector time with 43645 elements. Creating vector temp_frequency with 43645 elements. Creating vector time with 43645 elements. Creating vector flow2 with 43645 elements. Creating vector time with 43645 elements. Creating vector spare with 43645 elements. Creating vector time with 43645 elements. Creating vector salinity with 43645 elements. Creating vector time with 43645 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/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/2014/2014211/2014.211.03/isuslog.nc') Creating vector time with 8448 elements. Creating vector isusNitrate with 8448 elements. Creating vector time with 8448 elements. Creating vector isusTemp with 8448 elements. Creating vector time with 8448 elements. Creating vector isusQuality with 8448 elements. Creating vector time with 8448 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/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/2014/2014211/2014.211.03/biolume.nc') Creating vector time with 10757 elements. Creating vector rrr with 10757 elements. Creating vector time with 10757 elements. Creating vector cal_striing with 10757 elements. Creating vector time with 10757 elements. Creating vector avg_biolume with 10757 elements. Creating vector time with 10757 elements. Creating vector pump with 10757 elements. Creating vector time with 10757 elements. Creating vector system_voltage with 10757 elements. Creating vector time with 10757 elements. Creating vector flow with 10757 elements. Creating vector time with 10757 elements. Creating vector HV with 10757 elements. Creating vector time with 10757 elements. Creating vector reserved with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_0 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_1 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_2 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_3 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_4 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_5 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_6 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_7 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_8 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_9 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_10 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_11 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_12 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_13 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_14 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_15 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_16 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_17 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_18 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_19 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_20 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_21 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_22 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_23 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_24 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_25 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_26 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_27 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_28 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_29 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_30 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_31 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_32 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_33 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_34 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_35 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_36 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_37 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_38 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_39 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_40 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_41 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_42 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_43 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_44 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_45 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_46 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_47 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_48 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_49 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_50 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_51 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_52 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_53 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_54 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_55 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_56 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_57 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_58 with 10757 elements. Creating vector time with 10757 elements. Creating vector raw_59 with 10757 elements. Creating vector time with 10757 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/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/2014/2014211/2014.211.03/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (1005 x 994) with 998970 elements. Creating vector time with 1005 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (1005 x 994) with 998970 elements. Creating vector time with 1005 elements. Creating vector bin with 994 elements. Creating matrix countList (1005 x 994) with 998970 elements. Creating vector time with 1005 elements. Creating vector bin with 994 elements. Creating vector LCcount with 1005 elements. Creating vector time with 1005 elements. Creating vector transCount with 1005 elements. Creating vector time with 1005 elements. Creating vector nonTransCount with 1005 elements. Creating vector time with 1005 elements. Creating vector ai_mean with 1005 elements. Creating vector time with 1005 elements. Creating vector ai_min with 1005 elements. Creating vector time with 1005 elements. Creating vector ai_max with 1005 elements. Creating vector time with 1005 elements. Creating vector ai_std with 1005 elements. Creating vector time with 1005 elements. Creating vector esd_mean with 1005 elements. Creating vector time with 1005 elements. Creating vector esd_min with 1005 elements. Creating vector time with 1005 elements. Creating vector esd_max with 1005 elements. Creating vector time with 1005 elements. Creating vector esd_std with 1005 elements. Creating vector time with 1005 elements. Creating vector countSum with 1005 elements. Creating vector time with 1005 elements. Creating vector snapshot with 1005 elements. Creating vector time with 1005 elements. Creating vector threshold with 1005 elements. Creating vector time with 1005 elements. Creating vector sampleCount with 1005 elements. Creating vector time with 1005 elements. Creating vector flowCount with 1005 elements. Creating vector time with 1005 elements. Creating vector flowTime with 1005 elements. Creating vector time with 1005 elements. Creating vector bufferStatus with 1005 elements. Creating vector time with 1005 elements. Creating vector laserLevel with 1005 elements. Creating vector time with 1005 elements. Creating vector counter with 1005 elements. Creating vector time with 1005 elements. Creating vector counterPeriod with 1005 elements. Creating vector time with 1005 elements. Creating vector laserControl with 1005 elements. Creating vector time with 1005 elements. Creating vector countUnknownFrameCharacter with 1005 elements. Creating vector time with 1005 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 1005 elements. Creating vector time with 1005 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 1005 elements. Creating vector time with 1005 elements. Creating vector flowSpeed with 1005 elements. Creating vector time with 1005 elements. Creating vector countShortLFrameError with 1005 elements. Creating vector time with 1005 elements. Creating vector countGarbledLFrame with 1005 elements. Creating vector time with 1005 elements. Creating vector cFrameEsecs with 1005 elements. Creating vector time with 1005 elements. Creating vector correctedSampleCountList with 1005 elements. Creating vector time with 1005 elements. Creating vector time with 1005 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014211/2014.211.03/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.211.03.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_2014.211.03.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 4 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03.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 = 76 Gridding with nix = 228, iZ = 132 Using mean boxcar filter of vector... Using mean boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Gridding... T S O Using median boxcar filter of vector... Using median boxcar filter of vector... Using median boxcar filter of vector... bbp420 bbp700 fl700_uncorr N BL BLflow LOPC Only one good point or fewer - NaNing the gLOPCcount array. - NaNing the gLOPCtransCount array. - NaNing the gLOPCnonTransCount array. - NaNing the gLOPCLCcount array. Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB420 cvarname = gB700 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount No valid data for gLOPCcount cvarname = gLOPCtransCount No valid data for gLOPCtransCount cvarname = gLOPCnonTransCount No valid data for gLOPCnonTransCount cvarname = gLOPCLCcount No valid data for gLOPCLCcount Encountered 0 NaN values in array of lon that is 41934 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: Some input points were outside the grid domain(s). grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447) No depth array returned by grdtrack. Perhaps grdtrack could not be found in the search path. Setting ocean depths to 4000m for the track. Getting short wave radiation data from M1 for little plot above the biolume section plot Creating vector TIME with 118899 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 07/30/2014 09:30 to 07/30/2014 14:30 swr = NaN NaN NaN NaN NaN NaN Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03_swr.png [Warning: Contour not rendered for non-finite 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/2014211_GulperTimes.txt && touch ../results/2014211_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/2014/2014211/2014.211.03/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2014/2014211/2014.211.03/syslog -startEsecs 1406743499.6989 -surveyName Dorado389_2014_211_03_211_03 >> ../results/2014211_GulperTimes.txt Executing: removeGulpDups.py ../results/2014211_GulperTimes.txt Bottle: 0 Time: 1406744545 Depth: 4.4553 Dist: 1.0234 Bottle: 1 Time: 1406744891 Depth: 6.1085 Dist: 1.4639 Bottle: 2 Time: 1406745528 Depth: 44.1892 Dist: 2.2528 Bottle: 3 Time: 1406745999 Depth: 3.9986 Dist: 2.8709 Bottle: 4 Time: 1406746533 Depth: 6.036 Dist: 3.4573 Bottle: 5 Time: 1406749110 Depth: 4.4315 Dist: 6.3963 Bottle: 6 Time: 1406749455 Depth: 5.6855 Dist: 6.7781 Bottle: 7 Time: 1406750349 Depth: 8.8289 Dist: 7.7968 Bottle: 8 Time: 1406750595 Depth: 7.5184 Dist: 8.0749 Bottle: 9 Time: 1406750852 Depth: 5.6339 Dist: 8.3649 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03_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 2Column contouring gridded variable gT 2Column contouring gridded variable gS 2Column contouring gridded variable gN 2Column contouring gridded variable gO 2Column contouring gridded variable gB420 2Column contouring gridded variable gB700 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03_2column.png Elapsed time to save image: 6 seconds Biolume contouring gridded variable gD Biolume contouring gridded variable gT Biolume contouring gridded variable gS Biolume contouring gridded variable gN Biolume contouring gridded variable gO Biolume contouring gridded variable gB420 Biolume contouring gridded variable gB700 Biolume contouring gridded variable gF Biolume contouring gridded variable gBL Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03_biolume.png Elapsed time to save image: 24 seconds 2Column contouring gridded variable gLOPCcount 2Column contouring gridded variable gLOPCtransCount 2Column contouring gridded variable gLOPCnonTransCount 2Column contouring gridded variable gLOPCLCcount 2Column contouring gridded variable gT 2Column contouring gridded variable gB420 2Column contouring gridded variable gB700 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03_lopc.png Elapsed time to save image: 5 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_211_03_211_03_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03_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_211_03_211_03_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_211_03_211_03_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_211_03_211_03_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_211_03_211_03_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_211_03_211_03_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_Bioluminescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_211_03_211_03_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); Could not create .kmz for LOPC Total Count Creating Dorado389_2014_211_03_211_03.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03.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_211_03_211_03_Bioluminescence.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_211_03_211_03.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 2 NaNs found in bbpRed. Interpolating anyway. Encountered 1951 NaN values in array of lon that is 8448 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: Some input points were outside the grid domain(s). grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447) No depth array returned by grdtrack. Setting bottom depth to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03.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_211_03_211_03_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 ctd2 temperature... Interpolating ctd2 salinity... 2 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_211_03_211_03_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_211_03_211_03.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_211_03_211_03_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_211_03_211_03.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_211_03_211_03 processed" mccann@mbari.org < mail_Dorado389_2014_211_03_211_03.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.211.03.mat Processing time: 114 seconds