Execution of AUVprocess_main version 1.86 at 2018-05-24T19:59:58Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2013, ['275.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2013.275.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/ 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/2013/2013275/2013.275.00/navigation.nc') Creating vector time with 38687 elements. Creating vector mPos_x with 38687 elements. Creating vector time with 38687 elements. Creating vector mPos_y with 38687 elements. Creating vector time with 38687 elements. Creating vector mDepth with 38687 elements. Creating vector time with 38687 elements. Creating vector mGpsNorth with 38687 elements. Creating vector time with 38687 elements. Creating vector mGpsEast with 38687 elements. Creating vector time with 38687 elements. Creating vector mGpsValid with 38687 elements. Creating vector time with 38687 elements. Creating vector mPhi with 38687 elements. Creating vector time with 38687 elements. Creating vector mTheta with 38687 elements. Creating vector time with 38687 elements. Creating vector mPsi with 38687 elements. Creating vector time with 38687 elements. Creating vector mOmega_x with 38687 elements. Creating vector time with 38687 elements. Creating vector mOmega_y with 38687 elements. Creating vector time with 38687 elements. Creating vector mOmega_z with 38687 elements. Creating vector time with 38687 elements. Creating vector mPsaRange with 38687 elements. Creating vector time with 38687 elements. Creating vector mAltitude with 38687 elements. Creating vector time with 38687 elements. Creating vector mDvlAltitude with 38687 elements. Creating vector time with 38687 elements. Creating vector mEchoAltitude with 38687 elements. Creating vector time with 38687 elements. Creating vector mEchoHorizRange with 38687 elements. Creating vector time with 38687 elements. Creating vector mEchoAltitudeLast with 38687 elements. Creating vector time with 38687 elements. Creating vector mEchoHorizRangeLast with 38687 elements. Creating vector time with 38687 elements. Creating vector mEchoNumOfPings with 38687 elements. Creating vector time with 38687 elements. Creating vector mWaterSpeed with 38687 elements. Creating vector time with 38687 elements. Creating vector mDvlValid with 38687 elements. Creating vector time with 38687 elements. Creating vector mDvlNewData with 38687 elements. Creating vector time with 38687 elements. Creating vector mDeltaT with 38687 elements. Creating vector time with 38687 elements. Creating vector nfix with 38687 elements. Creating vector time with 38687 elements. Creating vector efix with 38687 elements. Creating vector time with 38687 elements. Creating vector filter_north with 38687 elements. Creating vector time with 38687 elements. Creating vector filter_east with 38687 elements. Creating vector time with 38687 elements. Creating vector filter_depth with 38687 elements. Creating vector time with 38687 elements. Creating vector north_current with 38687 elements. Creating vector time with 38687 elements. Creating vector east_current with 38687 elements. Creating vector time with 38687 elements. Creating vector speed_bias with 38687 elements. Creating vector time with 38687 elements. Creating vector heading_bias with 38687 elements. Creating vector time with 38687 elements. Creating vector latitude with 38687 elements. Creating vector time with 38687 elements. Creating vector longitude with 38687 elements. Creating vector time with 38687 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/navigation.nc'); processNav(): median of positive valued depths = 14 processNav(): Finding depths less than 98.0001 and times > 0 processNav(): length(Nav.depth) = 38687 processNav(): length(gindx) = 38687 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/2013/2013275/2013.275.00/gps.nc') Creating vector time with 573 elements. Creating vector hours with 573 elements. Creating vector time with 573 elements. Creating vector minutes with 573 elements. Creating vector time with 573 elements. Creating vector seconds with 573 elements. Creating vector time with 573 elements. Creating vector centiSeconds with 573 elements. Creating vector time with 573 elements. Creating vector latitude with 573 elements. Creating vector time with 573 elements. Creating vector longitude with 573 elements. Creating vector time with 573 elements. Creating vector quality with 573 elements. Creating vector time with 573 elements. Creating vector numberOfSatellites with 573 elements. Creating vector time with 573 elements. Creating vector hdop with 573 elements. Creating vector time with 573 elements. Creating vector antennaHeight with 573 elements. Creating vector time with 573 elements. Creating vector geoHeight with 573 elements. Creating vector time with 573 elements. Creating vector dgpsDataAge with 573 elements. Creating vector time with 573 elements. Creating vector dgpsRSID with 573 elements. Creating vector time with 573 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/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/2013/2013275/2013.275.00/parosci.nc') Creating vector time with 76442 elements. Creating vector depth with 76442 elements. Creating vector time with 76442 elements. Creating vector temp with 76442 elements. Creating vector time with 76442 elements. Creating vector pressure with 76442 elements. Creating vector time with 76442 elements. Creating vector temp_period with 76442 elements. Creating vector time with 76442 elements. Creating vector pres_period with 76442 elements. Creating vector time with 76442 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.22498 max(Depth.data) = 37.1542 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.22498 max(Depth.data) = 37.1542 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/2013/2013275/2013.275.00/hydroscatlog.nc') Creating vector time with 31043 elements. Creating vector Seconds with 31043 elements. Creating vector time with 31043 elements. Creating vector HundrethsOfSeconds with 31043 elements. Creating vector time with 31043 elements. Creating vector Snorm1 with 31043 elements. Creating vector time with 31043 elements. Creating vector Snorm2 with 31043 elements. Creating vector time with 31043 elements. Creating vector Snorm3 with 31043 elements. Creating vector time with 31043 elements. Creating vector Gain_Status_1 with 31043 elements. Creating vector time with 31043 elements. Creating vector Gain_Status_2 with 31043 elements. Creating vector time with 31043 elements. Creating vector Gain_Status_3 with 31043 elements. Creating vector time with 31043 elements. Creating vector RawDepthValue with 31043 elements. Creating vector time with 31043 elements. Creating vector RawTempValue with 31043 elements. Creating vector time with 31043 elements. Creating vector Temperature with 31043 elements. Creating vector time with 31043 elements. Creating vector ErrorValue with 31043 elements. Creating vector time with 31043 elements. Creating vector bb470 with 31043 elements. Creating vector time with 31043 elements. Creating vector bb676 with 31043 elements. Creating vector time with 31043 elements. Creating vector fl676u with 31043 elements. Creating vector time with 31043 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/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/2013/2013275/2013.275.00/ctdDriver.nc') Creating vector time with 30996 elements. Creating vector conductivity with 30996 elements. Creating vector time with 30996 elements. Creating vector temperature with 30996 elements. Creating vector time with 30996 elements. Creating vector cond_frequency with 30996 elements. Creating vector time with 30996 elements. Creating vector temp_frequency with 30996 elements. Creating vector time with 30996 elements. Creating vector spare with 30996 elements. Creating vector time with 30996 elements. Creating vector humidity with 30996 elements. Creating vector time with 30996 elements. Creating vector flow1 with 30996 elements. Creating vector time with 30996 elements. Creating vector CDOM with 30996 elements. Creating vector time with 30996 elements. Creating vector dissolvedO2 with 30996 elements. Creating vector time with 30996 elements. Creating vector salinity with 30996 elements. Creating vector time with 30996 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/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/2013/2013275/2013.275.00/ctdDriver2.nc') Creating vector time with 30994 elements. Creating vector conductivity with 30994 elements. Creating vector time with 30994 elements. Creating vector temperature with 30994 elements. Creating vector time with 30994 elements. Creating vector cond_frequency with 30994 elements. Creating vector time with 30994 elements. Creating vector temp_frequency with 30994 elements. Creating vector time with 30994 elements. Creating vector flow2 with 30994 elements. Creating vector time with 30994 elements. Creating vector spare with 30994 elements. Creating vector time with 30994 elements. Creating vector salinity with 30994 elements. Creating vector time with 30994 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/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/2013/2013275/2013.275.00/isuslog.nc') Creating vector time with 3 elements. Creating vector isusNitrate with 3 elements. Creating vector time with 3 elements. Creating vector isusTemp with 3 elements. Creating vector time with 3 elements. Creating vector isusQuality with 3 elements. Creating vector time with 3 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/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/2013/2013275/2013.275.00/biolume.nc') Creating vector time with 7645 elements. Creating vector rrr with 7645 elements. Creating vector time with 7645 elements. Creating vector cal_striing with 7645 elements. Creating vector time with 7645 elements. Creating vector avg_biolume with 7645 elements. Creating vector time with 7645 elements. Creating vector pump with 7645 elements. Creating vector time with 7645 elements. Creating vector system_voltage with 7645 elements. Creating vector time with 7645 elements. Creating vector flow with 7645 elements. Creating vector time with 7645 elements. Creating vector HV with 7645 elements. Creating vector time with 7645 elements. Creating vector reserved with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_0 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_1 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_2 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_3 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_4 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_5 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_6 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_7 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_8 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_9 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_10 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_11 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_12 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_13 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_14 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_15 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_16 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_17 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_18 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_19 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_20 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_21 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_22 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_23 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_24 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_25 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_26 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_27 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_28 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_29 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_30 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_31 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_32 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_33 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_34 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_35 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_36 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_37 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_38 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_39 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_40 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_41 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_42 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_43 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_44 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_45 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_46 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_47 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_48 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_49 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_50 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_51 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_52 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_53 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_54 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_55 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_56 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_57 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_58 with 7645 elements. Creating vector time with 7645 elements. Creating vector raw_59 with 7645 elements. Creating vector time with 7645 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/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/2013/2013275/2013.275.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (645 x 994) with 641130 elements. Creating vector time with 645 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (645 x 994) with 641130 elements. Creating vector time with 645 elements. Creating vector bin with 994 elements. Creating matrix countList (645 x 994) with 641130 elements. Creating vector time with 645 elements. Creating vector bin with 994 elements. Creating vector LCcount with 645 elements. Creating vector time with 645 elements. Creating vector transCount with 645 elements. Creating vector time with 645 elements. Creating vector nonTransCount with 645 elements. Creating vector time with 645 elements. Creating vector ai_mean with 645 elements. Creating vector time with 645 elements. Creating vector ai_min with 645 elements. Creating vector time with 645 elements. Creating vector ai_max with 645 elements. Creating vector time with 645 elements. Creating vector ai_std with 645 elements. Creating vector time with 645 elements. Creating vector esd_mean with 645 elements. Creating vector time with 645 elements. Creating vector esd_min with 645 elements. Creating vector time with 645 elements. Creating vector esd_max with 645 elements. Creating vector time with 645 elements. Creating vector esd_std with 645 elements. Creating vector time with 645 elements. Creating vector countSum with 645 elements. Creating vector time with 645 elements. Creating vector snapshot with 645 elements. Creating vector time with 645 elements. Creating vector threshold with 645 elements. Creating vector time with 645 elements. Creating vector sampleCount with 645 elements. Creating vector time with 645 elements. Creating vector flowCount with 645 elements. Creating vector time with 645 elements. Creating vector flowTime with 645 elements. Creating vector time with 645 elements. Creating vector bufferStatus with 645 elements. Creating vector time with 645 elements. Creating vector laserLevel with 645 elements. Creating vector time with 645 elements. Creating vector counter with 645 elements. Creating vector time with 645 elements. Creating vector counterPeriod with 645 elements. Creating vector time with 645 elements. Creating vector laserControl with 645 elements. Creating vector time with 645 elements. Creating vector countUnknownFrameCharacter with 645 elements. Creating vector time with 645 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 645 elements. Creating vector time with 645 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 645 elements. Creating vector time with 645 elements. Creating vector flowSpeed with 645 elements. Creating vector time with 645 elements. Creating vector countShortLFrameError with 645 elements. Creating vector time with 645 elements. Creating vector countGarbledLFrame with 645 elements. Creating vector time with 645 elements. Creating vector cFrameEsecs with 645 elements. Creating vector time with 645 elements. Creating vector correctedSampleCountList with 645 elements. Creating vector time with 645 elements. Creating vector time with 645 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013275/2013.275.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.275.00.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_2013.275.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 4 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_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 = 86 Gridding with nix = 258, iZ = 71 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 38153 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 38153 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 118897 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 10/02/2013 06:30 to 10/02/2013 10:29 swr = 2.3445 50.5823 180.7145 393.3453 539.3256 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2013275_GulperTimes.txt && touch ../results/2013275_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/2013/2013275/2013.275.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013275/2013.275.00/syslog -startEsecs 1380727044.1522 -surveyName Dorado389_2013_275_00_275_00 >> ../results/2013275_GulperTimes.txt Executing: removeGulpDups.py ../results/2013275_GulperTimes.txt Bottle: 0 Time: 1380728392 Depth: 2.9365 Dist: 1.6749 Bottle: 1 Time: 1380728935 Depth: 2.7668 Dist: 2.409 Bottle: 2 Time: 1380729518 Depth: 2.7707 Dist: 3.0538 Bottle: 3 Time: 1380730145 Depth: 2.8144 Dist: 3.905 Bottle: 4 Time: 1380730815 Depth: 2.8422 Dist: 4.814 Bottle: 5 Time: 1380731341 Depth: 2.6288 Dist: 5.3595 Bottle: 6 Time: 1380732018 Depth: 4.9501 Dist: 6.2564 Bottle: 7 Time: 1380732553 Depth: 9.8191 Dist: 6.9654 Bottle: 8 Time: 1380733276 Depth: 5.5012 Dist: 7.8329 Bottle: 9 Time: 1380733932 Depth: 11.5427 Dist: 8.6688 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_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 [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 852) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 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_2013_275_00_275_00_2column.png Elapsed time to save image: 9 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 [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1181) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 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_2013_275_00_275_00_biolume.png Elapsed time to save image: 32 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_2013_275_00_275_00_lopc.png Elapsed time to save image: 8 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_2013_275_00_275_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_2column.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2013/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_2013_275_00_275_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_275_00_275_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_275_00_275_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_275_00_275_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_275_00_275_00_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_275_00_275_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_275_00_275_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_275_00_275_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_275_00_275_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_275_00_275_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_275_00_275_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_275_00_275_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_275_00_275_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_275_00_275_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_275_00_275_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_275_00_275_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_275_00_275_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_275_00_275_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2013_275_00_275_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00.kml... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_275_00_275_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_2013_275_00_275_00.mat ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 202 NaNs found in bbpBlue. Interpolating anyway. 18 NaNs found in bbpRed. Interpolating anyway. Encountered 0 NaN values in array of lon that is 3100 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 3100 points from grid Monterey25.grd (2876 x 2447) Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00.txt... Copied to /mbari/AUVCTD/surveys/2013/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2013/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 202 NaNs found in bbpBlue. Interpolating anyway. 18 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2013/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_2013_275_00_275_00.nc... Copied to /mbari/AUVCTD/surveys/2013/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2013/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_275_00_275_00.mat... Copied to /mbari/AUVCTD/surveys/2013/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2013_275_00_275_00 processed" mccann@mbari.org < mail_Dorado389_2013_275_00_275_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.275.00.mat Processing time: 78 seconds