Execution of AUVprocess_main version 1.86 at 2018-05-24T15:02:51Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2012, ['157.07'], '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: 2012.157.07 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/ 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/2012/2012157/2012.157.07/navigation.nc') Creating vector time with 337821 elements. Creating vector mPos_x with 337821 elements. Creating vector time with 337821 elements. Creating vector mPos_y with 337821 elements. Creating vector time with 337821 elements. Creating vector mDepth with 337821 elements. Creating vector time with 337821 elements. Creating vector mGpsNorth with 337821 elements. Creating vector time with 337821 elements. Creating vector mGpsEast with 337821 elements. Creating vector time with 337821 elements. Creating vector mGpsValid with 337821 elements. Creating vector time with 337821 elements. Creating vector mPhi with 337821 elements. Creating vector time with 337821 elements. Creating vector mTheta with 337821 elements. Creating vector time with 337821 elements. Creating vector mPsi with 337821 elements. Creating vector time with 337821 elements. Creating vector mOmega_x with 337821 elements. Creating vector time with 337821 elements. Creating vector mOmega_y with 337821 elements. Creating vector time with 337821 elements. Creating vector mOmega_z with 337821 elements. Creating vector time with 337821 elements. Creating vector mPsaRange with 337821 elements. Creating vector time with 337821 elements. Creating vector mAltitude with 337821 elements. Creating vector time with 337821 elements. Creating vector mDvlAltitude with 337821 elements. Creating vector time with 337821 elements. Creating vector mEchoAltitude with 337821 elements. Creating vector time with 337821 elements. Creating vector mEchoHorizRange with 337821 elements. Creating vector time with 337821 elements. Creating vector mEchoAltitudeLast with 337821 elements. Creating vector time with 337821 elements. Creating vector mEchoHorizRangeLast with 337821 elements. Creating vector time with 337821 elements. Creating vector mEchoNumOfPings with 337821 elements. Creating vector time with 337821 elements. Creating vector mWaterSpeed with 337821 elements. Creating vector time with 337821 elements. Creating vector mDvlValid with 337821 elements. Creating vector time with 337821 elements. Creating vector mDvlNewData with 337821 elements. Creating vector time with 337821 elements. Creating vector mDeltaT with 337821 elements. Creating vector time with 337821 elements. Creating vector nfix with 337821 elements. Creating vector time with 337821 elements. Creating vector efix with 337821 elements. Creating vector time with 337821 elements. Creating vector filter_north with 337821 elements. Creating vector time with 337821 elements. Creating vector filter_east with 337821 elements. Creating vector time with 337821 elements. Creating vector filter_depth with 337821 elements. Creating vector time with 337821 elements. Creating vector north_current with 337821 elements. Creating vector time with 337821 elements. Creating vector east_current with 337821 elements. Creating vector time with 337821 elements. Creating vector speed_bias with 337821 elements. Creating vector time with 337821 elements. Creating vector heading_bias with 337821 elements. Creating vector time with 337821 elements. Creating vector latitude with 337821 elements. Creating vector time with 337821 elements. Creating vector longitude with 337821 elements. Creating vector time with 337821 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/navigation.nc'); processNav(): median of positive valued depths = 23.0671 processNav(): Finding depths less than 161.4697 and times > 0 processNav(): length(Nav.depth) = 337821 processNav(): length(gindx) = 337821 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/2012/2012157/2012.157.07/gps.nc') Creating vector time with 3367 elements. Creating vector hours with 3367 elements. Creating vector time with 3367 elements. Creating vector minutes with 3367 elements. Creating vector time with 3367 elements. Creating vector seconds with 3367 elements. Creating vector time with 3367 elements. Creating vector centiSeconds with 3367 elements. Creating vector time with 3367 elements. Creating vector latitude with 3367 elements. Creating vector time with 3367 elements. Creating vector longitude with 3367 elements. Creating vector time with 3367 elements. Creating vector quality with 3367 elements. Creating vector time with 3367 elements. Creating vector numberOfSatellites with 3367 elements. Creating vector time with 3367 elements. Creating vector hdop with 3367 elements. Creating vector time with 3367 elements. Creating vector antennaHeight with 3367 elements. Creating vector time with 3367 elements. Creating vector geoHeight with 3367 elements. Creating vector time with 3367 elements. Creating vector dgpsDataAge with 3367 elements. Creating vector time with 3367 elements. Creating vector dgpsRSID with 3367 elements. Creating vector time with 3367 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/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/2012/2012157/2012.157.07/parosci.nc') Creating vector time with 572897 elements. Creating vector depth with 572897 elements. Creating vector time with 572897 elements. Creating vector temp with 572897 elements. Creating vector time with 572897 elements. Creating vector pressure with 572897 elements. Creating vector time with 572897 elements. Creating vector temp_period with 572897 elements. Creating vector time with 572897 elements. Creating vector pres_period with 572897 elements. Creating vector time with 572897 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.33695 max(Depth.data) = 52.2591 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.33695 max(Depth.data) = 52.2591 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/2012/2012157/2012.157.07/hydroscatlog.nc') Creating vector time with 270252 elements. Creating vector Seconds with 270252 elements. Creating vector time with 270252 elements. Creating vector HundrethsOfSeconds with 270252 elements. Creating vector time with 270252 elements. Creating vector Snorm1 with 270252 elements. Creating vector time with 270252 elements. Creating vector Snorm2 with 270252 elements. Creating vector time with 270252 elements. Creating vector Snorm3 with 270252 elements. Creating vector time with 270252 elements. Creating vector Gain_Status_1 with 270252 elements. Creating vector time with 270252 elements. Creating vector Gain_Status_2 with 270252 elements. Creating vector time with 270252 elements. Creating vector Gain_Status_3 with 270252 elements. Creating vector time with 270252 elements. Creating vector RawDepthValue with 270252 elements. Creating vector time with 270252 elements. Creating vector RawTempValue with 270252 elements. Creating vector time with 270252 elements. Creating vector Temperature with 270252 elements. Creating vector time with 270252 elements. Creating vector ErrorValue with 270252 elements. Creating vector time with 270252 elements. Creating vector bb470 with 270252 elements. Creating vector time with 270252 elements. Creating vector bb676 with 270252 elements. Creating vector time with 270252 elements. Creating vector fl676u with 270252 elements. Creating vector time with 270252 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/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/2012/2012157/2012.157.07/ctdDriver.nc') Creating vector time with 270304 elements. Creating vector conductivity with 270304 elements. Creating vector time with 270304 elements. Creating vector temperature with 270304 elements. Creating vector time with 270304 elements. Creating vector cond_frequency with 270304 elements. Creating vector time with 270304 elements. Creating vector temp_frequency with 270304 elements. Creating vector time with 270304 elements. Creating vector spare with 270304 elements. Creating vector time with 270304 elements. Creating vector humidity with 270304 elements. Creating vector time with 270304 elements. Creating vector flow1 with 270304 elements. Creating vector time with 270304 elements. Creating vector CDOM with 270304 elements. Creating vector time with 270304 elements. Creating vector dissolvedO2 with 270304 elements. Creating vector time with 270304 elements. Creating vector salinity with 270304 elements. Creating vector time with 270304 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/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/2012/2012157/2012.157.07/ctdDriver2.nc') Creating vector time with 270299 elements. Creating vector conductivity with 270299 elements. Creating vector time with 270299 elements. Creating vector temperature with 270299 elements. Creating vector time with 270299 elements. Creating vector cond_frequency with 270299 elements. Creating vector time with 270299 elements. Creating vector temp_frequency with 270299 elements. Creating vector time with 270299 elements. Creating vector flow2 with 270299 elements. Creating vector time with 270299 elements. Creating vector spare with 270299 elements. Creating vector time with 270299 elements. Creating vector salinity with 270299 elements. Creating vector time with 270299 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/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/2012/2012157/2012.157.07/isuslog.nc') Creating vector time with 43327 elements. Creating vector isusNitrate with 43327 elements. Creating vector time with 43327 elements. Creating vector isusTemp with 43327 elements. Creating vector time with 43327 elements. Creating vector isusQuality with 43327 elements. Creating vector time with 43327 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/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/2012/2012157/2012.157.07/biolume.nc') Creating vector time with 66467 elements. Creating vector rrr with 66467 elements. Creating vector time with 66467 elements. Creating vector cal_striing with 66467 elements. Creating vector time with 66467 elements. Creating vector avg_biolume with 66467 elements. Creating vector time with 66467 elements. Creating vector pump with 66467 elements. Creating vector time with 66467 elements. Creating vector system_voltage with 66467 elements. Creating vector time with 66467 elements. Creating vector flow with 66467 elements. Creating vector time with 66467 elements. Creating vector HV with 66467 elements. Creating vector time with 66467 elements. Creating vector reserved with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_0 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_1 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_2 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_3 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_4 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_5 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_6 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_7 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_8 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_9 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_10 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_11 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_12 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_13 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_14 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_15 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_16 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_17 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_18 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_19 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_20 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_21 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_22 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_23 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_24 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_25 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_26 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_27 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_28 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_29 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_30 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_31 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_32 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_33 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_34 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_35 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_36 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_37 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_38 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_39 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_40 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_41 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_42 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_43 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_44 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_45 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_46 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_47 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_48 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_49 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_50 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_51 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_52 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_53 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_54 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_55 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_56 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_57 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_58 with 66467 elements. Creating vector time with 66467 elements. Creating vector raw_59 with 66467 elements. Creating vector time with 66467 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/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/2012/2012157/2012.157.07/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (5757 x 994) with 5722458 elements. Creating vector time with 5757 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (5757 x 994) with 5722458 elements. Creating vector time with 5757 elements. Creating vector bin with 994 elements. Creating matrix countList (5757 x 994) with 5722458 elements. Creating vector time with 5757 elements. Creating vector bin with 994 elements. Creating vector LCcount with 5757 elements. Creating vector time with 5757 elements. Creating vector transCount with 5757 elements. Creating vector time with 5757 elements. Creating vector nonTransCount with 5757 elements. Creating vector time with 5757 elements. Creating vector ai_mean with 5757 elements. Creating vector time with 5757 elements. Creating vector ai_min with 5757 elements. Creating vector time with 5757 elements. Creating vector ai_max with 5757 elements. Creating vector time with 5757 elements. Creating vector ai_std with 5757 elements. Creating vector time with 5757 elements. Creating vector esd_mean with 5757 elements. Creating vector time with 5757 elements. Creating vector esd_min with 5757 elements. Creating vector time with 5757 elements. Creating vector esd_max with 5757 elements. Creating vector time with 5757 elements. Creating vector esd_std with 5757 elements. Creating vector time with 5757 elements. Creating vector countSum with 5757 elements. Creating vector time with 5757 elements. Creating vector snapshot with 5757 elements. Creating vector time with 5757 elements. Creating vector threshold with 5757 elements. Creating vector time with 5757 elements. Creating vector sampleCount with 5757 elements. Creating vector time with 5757 elements. Creating vector flowCount with 5757 elements. Creating vector time with 5757 elements. Creating vector flowTime with 5757 elements. Creating vector time with 5757 elements. Creating vector bufferStatus with 5757 elements. Creating vector time with 5757 elements. Creating vector laserLevel with 5757 elements. Creating vector time with 5757 elements. Creating vector counter with 5757 elements. Creating vector time with 5757 elements. Creating vector counterPeriod with 5757 elements. Creating vector time with 5757 elements. Creating vector laserControl with 5757 elements. Creating vector time with 5757 elements. Creating vector countUnknownFrameCharacter with 5757 elements. Creating vector time with 5757 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 5757 elements. Creating vector time with 5757 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 5757 elements. Creating vector time with 5757 elements. Creating vector flowSpeed with 5757 elements. Creating vector time with 5757 elements. Creating vector countShortLFrameError with 5757 elements. Creating vector time with 5757 elements. Creating vector countGarbledLFrame with 5757 elements. Creating vector time with 5757 elements. Creating vector cFrameEsecs with 5757 elements. Creating vector time with 5757 elements. Creating vector correctedSampleCountList with 5757 elements. Creating vector time with 5757 elements. Creating vector time with 5757 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012157/2012.157.07/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012.157.07.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_2012.157.07.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 24 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07.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 = 464 Gridding with nix = 1392, iZ = 102 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 335193 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 335193 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 118893 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 06/05/2012 12:30 to 06/06/2012 08:30 swr = NaN 998.7999 932.8420 798.9486 584.9295 387.1884 213.8180 63.3471 6.8695 NaN NaN NaN NaN NaN NaN NaN NaN 6.3712 82.0976 257.0385 470.2123 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2012157_GulperTimes.txt && touch ../results/2012157_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/2012/2012157/2012.157.07/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2012/2012157/2012.157.07/syslog -startEsecs 1338930299.7351 -surveyName Dorado389_2012_157_07_157_07 >> ../results/2012157_GulperTimes.txt Executing: removeGulpDups.py ../results/2012157_GulperTimes.txt Bottle: 7 Time: 1338963309 Depth: 9.7593 Dist: 40.0843 Bottle: 8 Time: 1338963934 Depth: 11.1256 Dist: 40.7497 Bottle: 9 Time: 1338964526 Depth: 11.1256 Dist: 41.4232 Bottle: 3 Time: 1338993399 Depth: 2.5747 Dist: 74.77 Bottle: 0 Time: 1338995197 Depth: 2.9692 Dist: 76.7601 Bottle: 1 Time: 1338996924 Depth: 4.2255 Dist: 78.6674 Bottle: 2 Time: 1338997021 Depth: 16.4883 Dist: 78.7663 Bottle: 4 Time: 1338997324 Depth: 2.2487 Dist: 79.0682 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_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_2012_157_07_157_07_2column.png Elapsed time to save image: 14 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN Drawing bottom contour from EM300 data Biolume contouring gridded variable gO Drawing bottom contour from EM300 data Biolume contouring gridded variable gB420 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB700 Drawing bottom contour from EM300 data Biolume contouring gridded variable gF Drawing bottom contour from EM300 data Biolume contouring gridded variable gBL Drawing bottom contour from EM300 data Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_biolume.png Elapsed time to save image: 52 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_2012_157_07_157_07_lopc.png Elapsed time to save image: 13 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_2012_157_07_157_07_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_2column.png... Copied to /mbari/AUVCTD/surveys/2012/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_biolume.png... Copied to /mbari/AUVCTD/surveys/2012/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_lopc.png... Copied to /mbari/AUVCTD/surveys/2012/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2012/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2012/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2012/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_2012_157_07_157_07_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_157_07_157_07_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2012/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_2012_157_07_157_07_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_157_07_157_07_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2012/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_2012_157_07_157_07_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_157_07_157_07_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2012/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_2012_157_07_157_07_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_157_07_157_07_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2012/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_2012_157_07_157_07_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_157_07_157_07_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2012/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_2012_157_07_157_07_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_157_07_157_07_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2012/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_2012_157_07_157_07_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_157_07_157_07_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2012/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_2012_157_07_157_07_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_157_07_157_07_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2012/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_2012_157_07_157_07_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_157_07_157_07_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2012/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2012_157_07_157_07.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07.kml... Copied to /mbari/AUVCTD/surveys/2012/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_157_07_157_07_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_2012_157_07_157_07.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 15 NaNs found in bbpBlue. Interpolating anyway. 23 NaNs found in bbpRed. Interpolating anyway. 1 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 336 NaN values in array of lon that is 43327 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 42991 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 42991 are not equal to number of Lat lon points = 43327 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_2012_157_07_157_07.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07.txt... Copied to /mbari/AUVCTD/surveys/2012/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2012/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... 15 NaNs found in bbpBlue. Interpolating anyway. 23 NaNs found in bbpRed. Interpolating anyway. 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_2012_157_07_157_07_decim.nc... Copied to /mbari/AUVCTD/surveys/2012/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_2012_157_07_157_07.nc... Copied to /mbari/AUVCTD/surveys/2012/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07_gridded.mat... Copied to /mbari/AUVCTD/surveys/2012/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_157_07_157_07.mat... Copied to /mbari/AUVCTD/surveys/2012/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2012_157_07_157_07 processed" mccann@mbari.org < mail_Dorado389_2012_157_07_157_07.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012.157.07.mat Processing time: 633 seconds