Execution of AUVprocess_main version 1.86 at 2018-05-24T15:16:20Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2012, ['158.00'], '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: 2012.158.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/navigation.nc') Creating vector time with 334855 elements. Creating vector mPos_x with 334855 elements. Creating vector time with 334855 elements. Creating vector mPos_y with 334855 elements. Creating vector time with 334855 elements. Creating vector mDepth with 334855 elements. Creating vector time with 334855 elements. Creating vector mGpsNorth with 334855 elements. Creating vector time with 334855 elements. Creating vector mGpsEast with 334855 elements. Creating vector time with 334855 elements. Creating vector mGpsValid with 334855 elements. Creating vector time with 334855 elements. Creating vector mPhi with 334855 elements. Creating vector time with 334855 elements. Creating vector mTheta with 334855 elements. Creating vector time with 334855 elements. Creating vector mPsi with 334855 elements. Creating vector time with 334855 elements. Creating vector mOmega_x with 334855 elements. Creating vector time with 334855 elements. Creating vector mOmega_y with 334855 elements. Creating vector time with 334855 elements. Creating vector mOmega_z with 334855 elements. Creating vector time with 334855 elements. Creating vector mPsaRange with 334855 elements. Creating vector time with 334855 elements. Creating vector mAltitude with 334855 elements. Creating vector time with 334855 elements. Creating vector mDvlAltitude with 334855 elements. Creating vector time with 334855 elements. Creating vector mEchoAltitude with 334855 elements. Creating vector time with 334855 elements. Creating vector mEchoHorizRange with 334855 elements. Creating vector time with 334855 elements. Creating vector mEchoAltitudeLast with 334855 elements. Creating vector time with 334855 elements. Creating vector mEchoHorizRangeLast with 334855 elements. Creating vector time with 334855 elements. Creating vector mEchoNumOfPings with 334855 elements. Creating vector time with 334855 elements. Creating vector mWaterSpeed with 334855 elements. Creating vector time with 334855 elements. Creating vector mDvlValid with 334855 elements. Creating vector time with 334855 elements. Creating vector mDvlNewData with 334855 elements. Creating vector time with 334855 elements. Creating vector mDeltaT with 334855 elements. Creating vector time with 334855 elements. Creating vector nfix with 334855 elements. Creating vector time with 334855 elements. Creating vector efix with 334855 elements. Creating vector time with 334855 elements. Creating vector filter_north with 334855 elements. Creating vector time with 334855 elements. Creating vector filter_east with 334855 elements. Creating vector time with 334855 elements. Creating vector filter_depth with 334855 elements. Creating vector time with 334855 elements. Creating vector north_current with 334855 elements. Creating vector time with 334855 elements. Creating vector east_current with 334855 elements. Creating vector time with 334855 elements. Creating vector speed_bias with 334855 elements. Creating vector time with 334855 elements. Creating vector heading_bias with 334855 elements. Creating vector time with 334855 elements. Creating vector latitude with 334855 elements. Creating vector time with 334855 elements. Creating vector longitude with 334855 elements. Creating vector time with 334855 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/navigation.nc'); processNav(): median of positive valued depths = 22.3213 processNav(): Finding depths less than 156.2492 and times > 0 processNav(): length(Nav.depth) = 334855 processNav(): length(gindx) = 334855 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/2012/2012158/2012.158.00/gps.nc') Creating vector time with 5263 elements. Creating vector hours with 5263 elements. Creating vector time with 5263 elements. Creating vector minutes with 5263 elements. Creating vector time with 5263 elements. Creating vector seconds with 5263 elements. Creating vector time with 5263 elements. Creating vector centiSeconds with 5263 elements. Creating vector time with 5263 elements. Creating vector latitude with 5263 elements. Creating vector time with 5263 elements. Creating vector longitude with 5263 elements. Creating vector time with 5263 elements. Creating vector quality with 5263 elements. Creating vector time with 5263 elements. Creating vector numberOfSatellites with 5263 elements. Creating vector time with 5263 elements. Creating vector hdop with 5263 elements. Creating vector time with 5263 elements. Creating vector antennaHeight with 5263 elements. Creating vector time with 5263 elements. Creating vector geoHeight with 5263 elements. Creating vector time with 5263 elements. Creating vector dgpsDataAge with 5263 elements. Creating vector time with 5263 elements. Creating vector dgpsRSID with 5263 elements. Creating vector time with 5263 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/parosci.nc') Creating vector time with 567945 elements. Creating vector depth with 567945 elements. Creating vector time with 567945 elements. Creating vector temp with 567945 elements. Creating vector time with 567945 elements. Creating vector pressure with 567945 elements. Creating vector time with 567945 elements. Creating vector temp_period with 567945 elements. Creating vector time with 567945 elements. Creating vector pres_period with 567945 elements. Creating vector time with 567945 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.67337 max(Depth.data) = 59.956 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.67337 max(Depth.data) = 59.956 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/2012/2012158/2012.158.00/hydroscatlog.nc') Creating vector time with 267882 elements. Creating vector Seconds with 267882 elements. Creating vector time with 267882 elements. Creating vector HundrethsOfSeconds with 267882 elements. Creating vector time with 267882 elements. Creating vector Snorm1 with 267882 elements. Creating vector time with 267882 elements. Creating vector Snorm2 with 267882 elements. Creating vector time with 267882 elements. Creating vector Snorm3 with 267882 elements. Creating vector time with 267882 elements. Creating vector Gain_Status_1 with 267882 elements. Creating vector time with 267882 elements. Creating vector Gain_Status_2 with 267882 elements. Creating vector time with 267882 elements. Creating vector Gain_Status_3 with 267882 elements. Creating vector time with 267882 elements. Creating vector RawDepthValue with 267882 elements. Creating vector time with 267882 elements. Creating vector RawTempValue with 267882 elements. Creating vector time with 267882 elements. Creating vector Temperature with 267882 elements. Creating vector time with 267882 elements. Creating vector ErrorValue with 267882 elements. Creating vector time with 267882 elements. Creating vector bb470 with 267882 elements. Creating vector time with 267882 elements. Creating vector bb676 with 267882 elements. Creating vector time with 267882 elements. Creating vector fl676u with 267882 elements. Creating vector time with 267882 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/ctdDriver.nc') Creating vector time with 267787 elements. Creating vector conductivity with 267787 elements. Creating vector time with 267787 elements. Creating vector temperature with 267787 elements. Creating vector time with 267787 elements. Creating vector cond_frequency with 267787 elements. Creating vector time with 267787 elements. Creating vector temp_frequency with 267787 elements. Creating vector time with 267787 elements. Creating vector spare with 267787 elements. Creating vector time with 267787 elements. Creating vector humidity with 267787 elements. Creating vector time with 267787 elements. Creating vector flow1 with 267787 elements. Creating vector time with 267787 elements. Creating vector CDOM with 267787 elements. Creating vector time with 267787 elements. Creating vector dissolvedO2 with 267787 elements. Creating vector time with 267787 elements. Creating vector salinity with 267787 elements. Creating vector time with 267787 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/ctdDriver2.nc') Creating vector time with 267929 elements. Creating vector conductivity with 267929 elements. Creating vector time with 267929 elements. Creating vector temperature with 267929 elements. Creating vector time with 267929 elements. Creating vector cond_frequency with 267929 elements. Creating vector time with 267929 elements. Creating vector temp_frequency with 267929 elements. Creating vector time with 267929 elements. Creating vector flow2 with 267929 elements. Creating vector time with 267929 elements. Creating vector spare with 267929 elements. Creating vector time with 267929 elements. Creating vector salinity with 267929 elements. Creating vector time with 267929 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/isuslog.nc') Creating vector time with 42899 elements. Creating vector isusNitrate with 42899 elements. Creating vector time with 42899 elements. Creating vector isusTemp with 42899 elements. Creating vector time with 42899 elements. Creating vector isusQuality with 42899 elements. Creating vector time with 42899 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/biolume.nc') Creating vector time with 65884 elements. Creating vector rrr with 65884 elements. Creating vector time with 65884 elements. Creating vector cal_striing with 65884 elements. Creating vector time with 65884 elements. Creating vector avg_biolume with 65884 elements. Creating vector time with 65884 elements. Creating vector pump with 65884 elements. Creating vector time with 65884 elements. Creating vector system_voltage with 65884 elements. Creating vector time with 65884 elements. Creating vector flow with 65884 elements. Creating vector time with 65884 elements. Creating vector HV with 65884 elements. Creating vector time with 65884 elements. Creating vector reserved with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_0 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_1 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_2 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_3 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_4 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_5 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_6 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_7 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_8 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_9 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_10 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_11 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_12 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_13 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_14 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_15 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_16 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_17 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_18 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_19 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_20 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_21 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_22 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_23 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_24 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_25 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_26 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_27 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_28 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_29 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_30 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_31 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_32 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_33 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_34 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_35 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_36 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_37 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_38 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_39 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_40 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_41 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_42 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_43 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_44 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_45 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_46 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_47 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_48 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_49 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_50 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_51 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_52 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_53 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_54 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_55 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_56 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_57 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_58 with 65884 elements. Creating vector time with 65884 elements. Creating vector raw_59 with 65884 elements. Creating vector time with 65884 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/biolume.nc'); Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (5253 x 994) with 5221482 elements. Creating vector time with 5253 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (5253 x 994) with 5221482 elements. Creating vector time with 5253 elements. Creating vector bin with 994 elements. Creating matrix countList (5253 x 994) with 5221482 elements. Creating vector time with 5253 elements. Creating vector bin with 994 elements. Creating vector LCcount with 5253 elements. Creating vector time with 5253 elements. Creating vector transCount with 5253 elements. Creating vector time with 5253 elements. Creating vector nonTransCount with 5253 elements. Creating vector time with 5253 elements. Creating vector ai_mean with 5253 elements. Creating vector time with 5253 elements. Creating vector ai_min with 5253 elements. Creating vector time with 5253 elements. Creating vector ai_max with 5253 elements. Creating vector time with 5253 elements. Creating vector ai_std with 5253 elements. Creating vector time with 5253 elements. Creating vector esd_mean with 5253 elements. Creating vector time with 5253 elements. Creating vector esd_min with 5253 elements. Creating vector time with 5253 elements. Creating vector esd_max with 5253 elements. Creating vector time with 5253 elements. Creating vector esd_std with 5253 elements. Creating vector time with 5253 elements. Creating vector countSum with 5253 elements. Creating vector time with 5253 elements. Creating vector snapshot with 5253 elements. Creating vector time with 5253 elements. Creating vector threshold with 5253 elements. Creating vector time with 5253 elements. Creating vector sampleCount with 5253 elements. Creating vector time with 5253 elements. Creating vector flowCount with 5253 elements. Creating vector time with 5253 elements. Creating vector flowTime with 5253 elements. Creating vector time with 5253 elements. Creating vector bufferStatus with 5253 elements. Creating vector time with 5253 elements. Creating vector laserLevel with 5253 elements. Creating vector time with 5253 elements. Creating vector counter with 5253 elements. Creating vector time with 5253 elements. Creating vector counterPeriod with 5253 elements. Creating vector time with 5253 elements. Creating vector laserControl with 5253 elements. Creating vector time with 5253 elements. Creating vector countUnknownFrameCharacter with 5253 elements. Creating vector time with 5253 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 5253 elements. Creating vector time with 5253 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 5253 elements. Creating vector time with 5253 elements. Creating vector flowSpeed with 5253 elements. Creating vector time with 5253 elements. Creating vector countShortLFrameError with 5253 elements. Creating vector time with 5253 elements. Creating vector countGarbledLFrame with 5253 elements. Creating vector time with 5253 elements. Creating vector cFrameEsecs with 5253 elements. Creating vector time with 5253 elements. Creating vector correctedSampleCountList with 5253 elements. Creating vector time with 5253 elements. Creating vector time with 5253 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012158/2012.158.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012.158.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Calling build_auv_survey.m to construct survey file... SecondaryDissolvedO2 = [] Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012.158.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 26 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00.mat ************************************************************************* Calling plot_sections from ../viz to produce section plots ... Using median boxcar filter of vector... Using mean boxcar filter of vector... Number of profiles found = 452 Gridding with nix = 1356, iZ = 116 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 323516 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 323516 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: 06/06/2012 12:30 to 06/07/2012 09:30 swr = NaN 985.8397 941.2761 801.0302 596.1533 398.4271 186.8434 48.4050 8.0569 NaN NaN NaN NaN NaN NaN NaN NaN 4.7169 88.5655 278.5376 479.8693 636.2101 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2012158_GulperTimes.txt && touch ../results/2012158_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/2012/2012158/2012.158.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2012/2012158/2012.158.00/syslog -startEsecs 1339019676.0305 -surveyName Dorado389_2012_158_00_158_00 >> ../results/2012158_GulperTimes.txt Executing: removeGulpDups.py ../results/2012158_GulperTimes.txt Bottle: 7 Time: 1339053959 Depth: 10.0181 Dist: 43.0215 Bottle: 8 Time: 1339054489 Depth: 11.0664 Dist: 43.591 Bottle: 9 Time: 1339055093 Depth: 10.9971 Dist: 44.2387 Bottle: 3 Time: 1339082759 Depth: 3.8614 Dist: 76.176 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00_gridded.mat outvarstr = 'gF gT gN gS gD gO gB420 gB700 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth ' 2Column contouring gridded variable gD Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gS Drawing bottom contour from EM300 data 2Column contouring gridded variable gN Drawing bottom contour from EM300 data 2Column contouring gridded variable gO Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00_2column.png Elapsed time to save image: 22 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_158_00_158_00_biolume.png Elapsed time to save image: 61 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_158_00_158_00_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_158_00_158_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00_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_158_00_158_00_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_158_00_158_00_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_158_00_158_00_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_158_00_158_00_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_158_00_158_00_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_158_00_158_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_158_00_158_00_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_158_00_158_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_158_00_158_00_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_158_00_158_00_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_158_00_158_00_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_158_00_158_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_158_00_158_00_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_158_00_158_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_158_00_158_00_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_158_00_158_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_158_00_158_00_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_158_00_158_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_158_00_158_00_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_158_00_158_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_158_00_158_00_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_158_00_158_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_158_00_158_00_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_158_00_158_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00.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_158_00_158_00_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 414) In build_auv_survey (line 522) In AUVprocess_main (line 255)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 25 NaNs found in bbpBlue. Interpolating anyway. 33 NaNs found in bbpRed. Interpolating anyway. 2 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 1453 NaN values in array of lon that is 42899 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 41446 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 41446 are not equal to number of Lat lon points = 42899 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_158_00_158_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_158_00_158_00.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_158_00_158_00_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... 25 NaNs found in bbpBlue. Interpolating anyway. 33 NaNs found in bbpRed. Interpolating anyway. 2 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_158_00_158_00_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_158_00_158_00.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_158_00_158_00_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_158_00_158_00.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_158_00_158_00 processed" mccann@mbari.org < mail_Dorado389_2012_158_00_158_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012.158.00.mat Processing time: 697 seconds