Execution of AUVprocess_main version 1.86 at 2018-05-25T16:44:23Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2014, ['280.01'], '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: 2014.280.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/ 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/2014/2014280/2014.280.01/navigation.nc') Creating vector time with 118564 elements. Creating vector mPos_x with 118564 elements. Creating vector time with 118564 elements. Creating vector mPos_y with 118564 elements. Creating vector time with 118564 elements. Creating vector mDepth with 118564 elements. Creating vector time with 118564 elements. Creating vector mGpsNorth with 118564 elements. Creating vector time with 118564 elements. Creating vector mGpsEast with 118564 elements. Creating vector time with 118564 elements. Creating vector mGpsValid with 118564 elements. Creating vector time with 118564 elements. Creating vector mPhi with 118564 elements. Creating vector time with 118564 elements. Creating vector mTheta with 118564 elements. Creating vector time with 118564 elements. Creating vector mPsi with 118564 elements. Creating vector time with 118564 elements. Creating vector mOmega_x with 118564 elements. Creating vector time with 118564 elements. Creating vector mOmega_y with 118564 elements. Creating vector time with 118564 elements. Creating vector mOmega_z with 118564 elements. Creating vector time with 118564 elements. Creating vector mPsaRange with 118564 elements. Creating vector time with 118564 elements. Creating vector mAltitude with 118564 elements. Creating vector time with 118564 elements. Creating vector multibeamAltitude with 118564 elements. Creating vector time with 118564 elements. Creating vector mDvlAltitude with 118564 elements. Creating vector time with 118564 elements. Creating vector mEchoAltitude with 118564 elements. Creating vector time with 118564 elements. Creating vector mEchoHorizRange with 118564 elements. Creating vector time with 118564 elements. Creating vector mEchoAltitudeLast with 118564 elements. Creating vector time with 118564 elements. Creating vector mEchoHorizRangeLast with 118564 elements. Creating vector time with 118564 elements. Creating vector mEchoNumOfPings with 118564 elements. Creating vector time with 118564 elements. Creating vector nadirCnts with 118564 elements. Creating vector time with 118564 elements. Creating vector obstacleCnts with 118564 elements. Creating vector time with 118564 elements. Creating vector mWaterSpeed with 118564 elements. Creating vector time with 118564 elements. Creating vector mDvlValid with 118564 elements. Creating vector time with 118564 elements. Creating vector mDvlNewData with 118564 elements. Creating vector time with 118564 elements. Creating vector mDeltaT with 118564 elements. Creating vector time with 118564 elements. Creating vector nfix with 118564 elements. Creating vector time with 118564 elements. Creating vector efix with 118564 elements. Creating vector time with 118564 elements. Creating vector filter_north with 118564 elements. Creating vector time with 118564 elements. Creating vector filter_east with 118564 elements. Creating vector time with 118564 elements. Creating vector filter_depth with 118564 elements. Creating vector time with 118564 elements. Creating vector north_current with 118564 elements. Creating vector time with 118564 elements. Creating vector east_current with 118564 elements. Creating vector time with 118564 elements. Creating vector speed_bias with 118564 elements. Creating vector time with 118564 elements. Creating vector heading_bias with 118564 elements. Creating vector time with 118564 elements. Creating vector latitude with 118564 elements. Creating vector time with 118564 elements. Creating vector longitude with 118564 elements. Creating vector time with 118564 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/navigation.nc'); processNav(): median of positive valued depths = 31.5891 processNav(): Finding depths less than 221.1239 and times > 0 processNav(): length(Nav.depth) = 118564 processNav(): length(gindx) = 118564 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/2014/2014280/2014.280.01/gps.nc') Creating vector time with 2989 elements. Creating vector hours with 2989 elements. Creating vector time with 2989 elements. Creating vector minutes with 2989 elements. Creating vector time with 2989 elements. Creating vector seconds with 2989 elements. Creating vector time with 2989 elements. Creating vector centiSeconds with 2989 elements. Creating vector time with 2989 elements. Creating vector latitude with 2989 elements. Creating vector time with 2989 elements. Creating vector longitude with 2989 elements. Creating vector time with 2989 elements. Creating vector quality with 2989 elements. Creating vector time with 2989 elements. Creating vector numberOfSatellites with 2989 elements. Creating vector time with 2989 elements. Creating vector hdop with 2989 elements. Creating vector time with 2989 elements. Creating vector antennaHeight with 2989 elements. Creating vector time with 2989 elements. Creating vector geoHeight with 2989 elements. Creating vector time with 2989 elements. Creating vector dgpsDataAge with 2989 elements. Creating vector time with 2989 elements. Creating vector dgpsRSID with 2989 elements. Creating vector time with 2989 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/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/2014/2014280/2014.280.01/parosci.nc') Creating vector time with 233144 elements. Creating vector depth with 233144 elements. Creating vector time with 233144 elements. Creating vector temp with 233144 elements. Creating vector time with 233144 elements. Creating vector pressure with 233144 elements. Creating vector time with 233144 elements. Creating vector temp_period with 233144 elements. Creating vector time with 233144 elements. Creating vector pres_period with 233144 elements. Creating vector time with 233144 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.36412 max(Depth.data) = 62.6382 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.36412 max(Depth.data) = 62.6382 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/2014/2014280/2014.280.01/hydroscatlog.nc') Creating vector time with 95001 elements. Creating vector Seconds with 95001 elements. Creating vector time with 95001 elements. Creating vector HundrethsOfSeconds with 95001 elements. Creating vector time with 95001 elements. Creating vector Snorm1 with 95001 elements. Creating vector time with 95001 elements. Creating vector Snorm2 with 95001 elements. Creating vector time with 95001 elements. Creating vector Snorm3 with 95001 elements. Creating vector time with 95001 elements. Creating vector Gain_Status_1 with 95001 elements. Creating vector time with 95001 elements. Creating vector Gain_Status_2 with 95001 elements. Creating vector time with 95001 elements. Creating vector Gain_Status_3 with 95001 elements. Creating vector time with 95001 elements. Creating vector RawDepthValue with 95001 elements. Creating vector time with 95001 elements. Creating vector RawTempValue with 95001 elements. Creating vector time with 95001 elements. Creating vector Temperature with 95001 elements. Creating vector time with 95001 elements. Creating vector ErrorValue with 95001 elements. Creating vector time with 95001 elements. Creating vector bb470 with 95001 elements. Creating vector time with 95001 elements. Creating vector bb676 with 95001 elements. Creating vector time with 95001 elements. Creating vector fl676u with 95001 elements. Creating vector time with 95001 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/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/2014/2014280/2014.280.01/ctdDriver.nc') Creating vector time with 94969 elements. Creating vector conductivity with 94969 elements. Creating vector time with 94969 elements. Creating vector temperature with 94969 elements. Creating vector time with 94969 elements. Creating vector cond_frequency with 94969 elements. Creating vector time with 94969 elements. Creating vector temp_frequency with 94969 elements. Creating vector time with 94969 elements. Creating vector spare with 94969 elements. Creating vector time with 94969 elements. Creating vector humidity with 94969 elements. Creating vector time with 94969 elements. Creating vector flow1 with 94969 elements. Creating vector time with 94969 elements. Creating vector CDOM with 94969 elements. Creating vector time with 94969 elements. Creating vector dissolvedO2 with 94969 elements. Creating vector time with 94969 elements. Creating vector salinity with 94969 elements. Creating vector time with 94969 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/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/2014/2014280/2014.280.01/ctdDriver2.nc') Creating vector time with 94970 elements. Creating vector conductivity with 94970 elements. Creating vector time with 94970 elements. Creating vector temperature with 94970 elements. Creating vector time with 94970 elements. Creating vector cond_frequency with 94970 elements. Creating vector time with 94970 elements. Creating vector temp_frequency with 94970 elements. Creating vector time with 94970 elements. Creating vector rhodamine with 94970 elements. Creating vector time with 94970 elements. Creating vector flow2 with 94970 elements. Creating vector time with 94970 elements. Creating vector spare with 94970 elements. Creating vector time with 94970 elements. Creating vector salinity with 94970 elements. Creating vector time with 94970 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/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/2014/2014280/2014.280.01/isuslog.nc') Creating vector time with 18424 elements. Creating vector isusNitrate with 18424 elements. Creating vector time with 18424 elements. Creating vector isusTemp with 18424 elements. Creating vector time with 18424 elements. Creating vector isusQuality with 18424 elements. Creating vector time with 18424 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/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/2014/2014280/2014.280.01/biolume.nc') Creating vector time with 23364 elements. Creating vector rrr with 23364 elements. Creating vector time with 23364 elements. Creating vector cal_striing with 23364 elements. Creating vector time with 23364 elements. Creating vector avg_biolume with 23364 elements. Creating vector time with 23364 elements. Creating vector pump with 23364 elements. Creating vector time with 23364 elements. Creating vector system_voltage with 23364 elements. Creating vector time with 23364 elements. Creating vector flow with 23364 elements. Creating vector time with 23364 elements. Creating vector HV with 23364 elements. Creating vector time with 23364 elements. Creating vector reserved with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_0 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_1 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_2 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_3 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_4 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_5 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_6 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_7 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_8 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_9 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_10 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_11 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_12 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_13 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_14 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_15 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_16 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_17 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_18 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_19 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_20 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_21 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_22 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_23 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_24 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_25 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_26 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_27 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_28 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_29 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_30 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_31 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_32 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_33 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_34 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_35 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_36 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_37 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_38 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_39 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_40 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_41 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_42 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_43 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_44 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_45 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_46 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_47 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_48 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_49 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_50 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_51 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_52 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_53 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_54 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_55 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_56 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_57 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_58 with 23364 elements. Creating vector time with 23364 elements. Creating vector raw_59 with 23364 elements. Creating vector time with 23364 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/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/2014/2014280/2014.280.01/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (2144 x 994) with 2131136 elements. Creating vector time with 2144 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (2144 x 994) with 2131136 elements. Creating vector time with 2144 elements. Creating vector bin with 994 elements. Creating matrix countList (2144 x 994) with 2131136 elements. Creating vector time with 2144 elements. Creating vector bin with 994 elements. Creating vector LCcount with 2144 elements. Creating vector time with 2144 elements. Creating vector transCount with 2144 elements. Creating vector time with 2144 elements. Creating vector nonTransCount with 2144 elements. Creating vector time with 2144 elements. Creating vector ai_mean with 2144 elements. Creating vector time with 2144 elements. Creating vector ai_min with 2144 elements. Creating vector time with 2144 elements. Creating vector ai_max with 2144 elements. Creating vector time with 2144 elements. Creating vector ai_std with 2144 elements. Creating vector time with 2144 elements. Creating vector esd_mean with 2144 elements. Creating vector time with 2144 elements. Creating vector esd_min with 2144 elements. Creating vector time with 2144 elements. Creating vector esd_max with 2144 elements. Creating vector time with 2144 elements. Creating vector esd_std with 2144 elements. Creating vector time with 2144 elements. Creating vector countSum with 2144 elements. Creating vector time with 2144 elements. Creating vector snapshot with 2144 elements. Creating vector time with 2144 elements. Creating vector threshold with 2144 elements. Creating vector time with 2144 elements. Creating vector sampleCount with 2144 elements. Creating vector time with 2144 elements. Creating vector flowCount with 2144 elements. Creating vector time with 2144 elements. Creating vector flowTime with 2144 elements. Creating vector time with 2144 elements. Creating vector bufferStatus with 2144 elements. Creating vector time with 2144 elements. Creating vector laserLevel with 2144 elements. Creating vector time with 2144 elements. Creating vector counter with 2144 elements. Creating vector time with 2144 elements. Creating vector counterPeriod with 2144 elements. Creating vector time with 2144 elements. Creating vector laserControl with 2144 elements. Creating vector time with 2144 elements. Creating vector countUnknownFrameCharacter with 2144 elements. Creating vector time with 2144 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 2144 elements. Creating vector time with 2144 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 2144 elements. Creating vector time with 2144 elements. Creating vector flowSpeed with 2144 elements. Creating vector time with 2144 elements. Creating vector countShortLFrameError with 2144 elements. Creating vector time with 2144 elements. Creating vector countGarbledLFrame with 2144 elements. Creating vector time with 2144 elements. Creating vector cFrameEsecs with 2144 elements. Creating vector time with 2144 elements. Creating vector correctedSampleCountList with 2144 elements. Creating vector time with 2144 elements. Creating vector time with 2144 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014280/2014.280.01/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.280.01.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_2014.280.01.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_280_01_280_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_280_01_280_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_280_01_280_01.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 = 142 Gridding with nix = 426, iZ = 122 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 113199 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 113199 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: 10/07/2014 07:29 to 10/07/2014 16:29 swr = 13.3375 66.6150 149.7776 257.6926 419.0027 822.5903 790.8659 687.3030 308.2878 223.5671 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_280_01_280_01_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/2014280_GulperTimes.txt && touch ../results/2014280_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/2014/2014280/2014.280.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2014/2014280/2014.280.01/syslog -startEsecs 1412699623.7318 -surveyName Dorado389_2014_280_01_280_01 >> ../results/2014280_GulperTimes.txt Executing: removeGulpDups.py ../results/2014280_GulperTimes.txt Bottle: 0 Time: 1412699952.46 Depth: 25.716 Dist: 0.28534 Bottle: 1 Time: 1412700795.66 Depth: 12.8612 Dist: 1.1025 Bottle: 2 Time: 1412701579.26 Depth: 28.8938 Dist: 1.9169 Bottle: 3 Time: 1412703674.86 Depth: 30.1437 Dist: 4.0408 Bottle: 4 Time: 1412704419.46 Depth: 27.9865 Dist: 4.8836 Bottle: 5 Time: 1412705701.26 Depth: 24.6101 Dist: 6.3416 Bottle: 6 Time: 1412706440.66 Depth: 35.0468 Dist: 7.175 Bottle: 7 Time: 1412707666.06 Depth: 26.133 Dist: 8.4045 Bottle: 8 Time: 1412708177.86 Depth: 18.8767 Dist: 9.066 Bottle: 9 Time: 1412709709.06 Depth: 27.1575 Dist: 11.3748 Bottle: 10 Time: 1412710280.66 Depth: 13.4529 Dist: 12.2422 Bottle: 11 Time: 1412711642.06 Depth: 19.7851 Dist: 14.3082 Bottle: 12 Time: 1412712162.26 Depth: 19.7682 Dist: 15.1311 Bottle: 13 Time: 1412713687.86 Depth: 22.0467 Dist: 16.8992 Bottle: 14 Time: 1412714309.06 Depth: 16.8603 Dist: 17.4482 Bottle: 15 Time: 1412715767.26 Depth: 15.0156 Dist: 18.8528 Bottle: 16 Time: 1412716685.26 Depth: 22.0943 Dist: 19.8239 Bottle: 17 Time: 1412717745.66 Depth: 19.3374 Dist: 20.9356 Bottle: 18 Time: 1412718598.06 Depth: 15.8754 Dist: 21.7248 Bottle: 19 Time: 1412719637.86 Depth: 30.648 Dist: 22.8099 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_280_01_280_01_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_280_01_280_01_2column.png Elapsed time to save image: 7 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_280_01_280_01_biolume.png Elapsed time to save image: 36 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_280_01_280_01_lopc.png Elapsed time to save image: 9 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_280_01_280_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_280_01_280_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_280_01_280_01_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_280_01_280_01_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_280_01_280_01_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_280_01_280_01_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_280_01_280_01_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_280_01_280_01_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_280_01_280_01_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_280_01_280_01_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_280_01_280_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_280_01_280_01_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_280_01_280_01_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_280_01_280_01_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_280_01_280_01_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_280_01_280_01_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_280_01_280_01_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_280_01_280_01_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_280_01_280_01_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_280_01_280_01_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_280_01_280_01_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_280_01_280_01_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_280_01_280_01_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_280_01_280_01_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_280_01_280_01_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_280_01_280_01_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_280_01_280_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_280_01_280_01.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_280_01_280_01_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_280_01_280_01.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 21 NaNs found in bbpBlue. Interpolating anyway. 23 NaNs found in bbpRed. Interpolating anyway. Encountered 837 NaN values in array of lon that is 18424 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 17587 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 17587 are not equal to number of Lat lon points = 18424 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_280_01_280_01.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_280_01_280_01_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_280_01_280_01.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_280_01_280_01_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... 21 NaNs found in bbpBlue. Interpolating anyway. 23 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_280_01_280_01_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_280_01_280_01.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_280_01_280_01_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_280_01_280_01.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_280_01_280_01 processed" mccann@mbari.org < mail_Dorado389_2014_280_01_280_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.280.01.mat Processing time: 162 seconds