Execution of AUVprocess_main version 1.86 at 2018-05-24T00:53:17Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2011, ['165.00'], '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: 2011.165.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/ 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/2011/2011165/2011.165.00/navigation.nc') Creating vector time with 327089 elements. Creating vector mPos_x with 327089 elements. Creating vector time with 327089 elements. Creating vector mPos_y with 327089 elements. Creating vector time with 327089 elements. Creating vector mDepth with 327089 elements. Creating vector time with 327089 elements. Creating vector mGpsNorth with 327089 elements. Creating vector time with 327089 elements. Creating vector mGpsEast with 327089 elements. Creating vector time with 327089 elements. Creating vector mGpsValid with 327089 elements. Creating vector time with 327089 elements. Creating vector mPhi with 327089 elements. Creating vector time with 327089 elements. Creating vector mTheta with 327089 elements. Creating vector time with 327089 elements. Creating vector mPsi with 327089 elements. Creating vector time with 327089 elements. Creating vector mOmega_x with 327089 elements. Creating vector time with 327089 elements. Creating vector mOmega_y with 327089 elements. Creating vector time with 327089 elements. Creating vector mOmega_z with 327089 elements. Creating vector time with 327089 elements. Creating vector mPsaRange with 327089 elements. Creating vector time with 327089 elements. Creating vector mAltitude with 327089 elements. Creating vector time with 327089 elements. Creating vector mDvlAltitude with 327089 elements. Creating vector time with 327089 elements. Creating vector mEchoAltitude with 327089 elements. Creating vector time with 327089 elements. Creating vector mEchoHorizRange with 327089 elements. Creating vector time with 327089 elements. Creating vector mEchoAltitudeLast with 327089 elements. Creating vector time with 327089 elements. Creating vector mEchoHorizRangeLast with 327089 elements. Creating vector time with 327089 elements. Creating vector mEchoNumOfPings with 327089 elements. Creating vector time with 327089 elements. Creating vector mWaterSpeed with 327089 elements. Creating vector time with 327089 elements. Creating vector mDvlValid with 327089 elements. Creating vector time with 327089 elements. Creating vector mDvlNewData with 327089 elements. Creating vector time with 327089 elements. Creating vector mDeltaT with 327089 elements. Creating vector time with 327089 elements. Creating vector nfix with 327089 elements. Creating vector time with 327089 elements. Creating vector efix with 327089 elements. Creating vector time with 327089 elements. Creating vector filter_north with 327089 elements. Creating vector time with 327089 elements. Creating vector filter_east with 327089 elements. Creating vector time with 327089 elements. Creating vector filter_depth with 327089 elements. Creating vector time with 327089 elements. Creating vector north_current with 327089 elements. Creating vector time with 327089 elements. Creating vector east_current with 327089 elements. Creating vector time with 327089 elements. Creating vector speed_bias with 327089 elements. Creating vector time with 327089 elements. Creating vector heading_bias with 327089 elements. Creating vector time with 327089 elements. Creating vector latitude with 327089 elements. Creating vector time with 327089 elements. Creating vector longitude with 327089 elements. Creating vector time with 327089 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/navigation.nc'); processNav(): median of positive valued depths = 13.445 processNav(): Finding depths less than 94.115 and times > 0 processNav(): length(Nav.depth) = 327089 processNav(): length(gindx) = 327089 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/2011/2011165/2011.165.00/gps.nc') Creating vector time with 1558 elements. Creating vector hours with 1558 elements. Creating vector time with 1558 elements. Creating vector minutes with 1558 elements. Creating vector time with 1558 elements. Creating vector seconds with 1558 elements. Creating vector time with 1558 elements. Creating vector centiSeconds with 1558 elements. Creating vector time with 1558 elements. Creating vector latitude with 1558 elements. Creating vector time with 1558 elements. Creating vector longitude with 1558 elements. Creating vector time with 1558 elements. Creating vector quality with 1558 elements. Creating vector time with 1558 elements. Creating vector numberOfSatellites with 1558 elements. Creating vector time with 1558 elements. Creating vector hdop with 1558 elements. Creating vector time with 1558 elements. Creating vector antennaHeight with 1558 elements. Creating vector time with 1558 elements. Creating vector geoHeight with 1558 elements. Creating vector time with 1558 elements. Creating vector dgpsDataAge with 1558 elements. Creating vector time with 1558 elements. Creating vector dgpsRSID with 1558 elements. Creating vector time with 1558 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/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/2011/2011165/2011.165.00/parosci.nc') Creating vector time with 554673 elements. Creating vector depth with 554673 elements. Creating vector time with 554673 elements. Creating vector temp with 554673 elements. Creating vector time with 554673 elements. Creating vector pressure with 554673 elements. Creating vector time with 554673 elements. Creating vector temp_period with 554673 elements. Creating vector time with 554673 elements. Creating vector pres_period with 554673 elements. Creating vector time with 554673 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.89071 max(Depth.data) = 25.0273 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.89071 max(Depth.data) = 25.0273 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/2011/2011165/2011.165.00/hydroscatlog.nc') Creating vector time with 261673 elements. Creating vector Seconds with 261673 elements. Creating vector time with 261673 elements. Creating vector HundrethsOfSeconds with 261673 elements. Creating vector time with 261673 elements. Creating vector Snorm1 with 261673 elements. Creating vector time with 261673 elements. Creating vector Snorm2 with 261673 elements. Creating vector time with 261673 elements. Creating vector Snorm3 with 261673 elements. Creating vector time with 261673 elements. Creating vector Gain_Status_1 with 261673 elements. Creating vector time with 261673 elements. Creating vector Gain_Status_2 with 261673 elements. Creating vector time with 261673 elements. Creating vector Gain_Status_3 with 261673 elements. Creating vector time with 261673 elements. Creating vector RawDepthValue with 261673 elements. Creating vector time with 261673 elements. Creating vector RawTempValue with 261673 elements. Creating vector time with 261673 elements. Creating vector Temperature with 261673 elements. Creating vector time with 261673 elements. Creating vector ErrorValue with 261673 elements. Creating vector time with 261673 elements. Creating vector bb470 with 261673 elements. Creating vector time with 261673 elements. Creating vector bb676 with 261673 elements. Creating vector time with 261673 elements. Creating vector fl676u with 261673 elements. Creating vector time with 261673 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/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/2011/2011165/2011.165.00/ctdDriver.nc') Creating vector time with 261629 elements. Creating vector conductivity with 261629 elements. Creating vector time with 261629 elements. Creating vector temperature with 261629 elements. Creating vector time with 261629 elements. Creating vector cond_frequency with 261629 elements. Creating vector time with 261629 elements. Creating vector temp_frequency with 261629 elements. Creating vector time with 261629 elements. Creating vector spare with 261629 elements. Creating vector time with 261629 elements. Creating vector humidity with 261629 elements. Creating vector time with 261629 elements. Creating vector flow1 with 261629 elements. Creating vector time with 261629 elements. Creating vector CDOM with 261629 elements. Creating vector time with 261629 elements. Creating vector dissolvedO2 with 261629 elements. Creating vector time with 261629 elements. Creating vector salinity with 261629 elements. Creating vector time with 261629 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/ctdDriver.cfg ScaleFactor = 0.1410 DarkCounts = 55 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/2011/2011165/2011.165.00/ctdDriver2.nc') Creating vector time with 261725 elements. Creating vector conductivity with 261725 elements. Creating vector time with 261725 elements. Creating vector temperature with 261725 elements. Creating vector time with 261725 elements. Creating vector cond_frequency with 261725 elements. Creating vector time with 261725 elements. Creating vector temp_frequency with 261725 elements. Creating vector time with 261725 elements. Creating vector flow2 with 261725 elements. Creating vector time with 261725 elements. Creating vector spare with 261725 elements. Creating vector time with 261725 elements. Creating vector salinity with 261725 elements. Creating vector time with 261725 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/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/2011/2011165/2011.165.00/isuslog.nc') Creating vector time with 64980 elements. Creating vector isusNitrate with 64980 elements. Creating vector time with 64980 elements. Creating vector isusTemp with 64980 elements. Creating vector time with 64980 elements. Creating vector isusQuality with 64980 elements. Creating vector time with 64980 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/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/2011/2011165/2011.165.00/biolume.nc') Creating vector time with 64358 elements. Creating vector rrr with 64358 elements. Creating vector time with 64358 elements. Creating vector cal_striing with 64358 elements. Creating vector time with 64358 elements. Creating vector avg_biolume with 64358 elements. Creating vector time with 64358 elements. Creating vector pump with 64358 elements. Creating vector time with 64358 elements. Creating vector system_voltage with 64358 elements. Creating vector time with 64358 elements. Creating vector flow with 64358 elements. Creating vector time with 64358 elements. Creating vector HV with 64358 elements. Creating vector time with 64358 elements. Creating vector reserved with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_0 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_1 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_2 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_3 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_4 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_5 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_6 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_7 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_8 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_9 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_10 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_11 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_12 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_13 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_14 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_15 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_16 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_17 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_18 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_19 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_20 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_21 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_22 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_23 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_24 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_25 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_26 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_27 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_28 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_29 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_30 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_31 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_32 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_33 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_34 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_35 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_36 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_37 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_38 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_39 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_40 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_41 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_42 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_43 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_44 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_45 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_46 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_47 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_48 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_49 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_50 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_51 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_52 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_53 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_54 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_55 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_56 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_57 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_58 with 64358 elements. Creating vector time with 64358 elements. Creating vector raw_59 with 64358 elements. Creating vector time with 64358 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/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/2011/2011165/2011.165.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (4736 x 994) with 4707584 elements. Creating vector time with 4736 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (4736 x 994) with 4707584 elements. Creating vector time with 4736 elements. Creating vector bin with 994 elements. Creating matrix countList (4736 x 994) with 4707584 elements. Creating vector time with 4736 elements. Creating vector bin with 994 elements. Creating vector LCcount with 4736 elements. Creating vector time with 4736 elements. Creating vector transCount with 4736 elements. Creating vector time with 4736 elements. Creating vector nonTransCount with 4736 elements. Creating vector time with 4736 elements. Creating vector ai_mean with 4736 elements. Creating vector time with 4736 elements. Creating vector ai_min with 4736 elements. Creating vector time with 4736 elements. Creating vector ai_max with 4736 elements. Creating vector time with 4736 elements. Creating vector ai_std with 4736 elements. Creating vector time with 4736 elements. Creating vector esd_mean with 4736 elements. Creating vector time with 4736 elements. Creating vector esd_min with 4736 elements. Creating vector time with 4736 elements. Creating vector esd_max with 4736 elements. Creating vector time with 4736 elements. Creating vector esd_std with 4736 elements. Creating vector time with 4736 elements. Creating vector countSum with 4736 elements. Creating vector time with 4736 elements. Creating vector snapshot with 4736 elements. Creating vector time with 4736 elements. Creating vector threshold with 4736 elements. Creating vector time with 4736 elements. Creating vector sampleCount with 4736 elements. Creating vector time with 4736 elements. Creating vector flowCount with 4736 elements. Creating vector time with 4736 elements. Creating vector flowTime with 4736 elements. Creating vector time with 4736 elements. Creating vector bufferStatus with 4736 elements. Creating vector time with 4736 elements. Creating vector laserLevel with 4736 elements. Creating vector time with 4736 elements. Creating vector counter with 4736 elements. Creating vector time with 4736 elements. Creating vector counterPeriod with 4736 elements. Creating vector time with 4736 elements. Creating vector laserControl with 4736 elements. Creating vector time with 4736 elements. Creating vector countUnknownFrameCharacter with 4736 elements. Creating vector time with 4736 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 4736 elements. Creating vector time with 4736 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 4736 elements. Creating vector time with 4736 elements. Creating vector flowSpeed with 4736 elements. Creating vector time with 4736 elements. Creating vector countShortLFrameError with 4736 elements. Creating vector time with 4736 elements. Creating vector countGarbledLFrame with 4736 elements. Creating vector time with 4736 elements. Creating vector cFrameEsecs with 4736 elements. Creating vector time with 4736 elements. Creating vector correctedSampleCountList with 4736 elements. Creating vector time with 4736 elements. Creating vector time with 4736 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011165/2011.165.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011.165.00.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_2011.165.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 21 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_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 = 458 Gridding with nix = 1374, iZ = 47 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 290950 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 290950 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 118879 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 06/14/2011 12:30 to 06/15/2011 09:30 swr = NaN 999.9000 920.5051 776.9838 623.6321 418.4512 255.7095 84.5613 8.7624 1.8666 1.7826 1.7999 1.7318 1.8873 1.5175 1.5968 1.5524 3.9915 88.0562 318.0013 371.1904 485.8581 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2011165_GulperTimes.txt && touch ../results/2011165_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/2011/2011165/2011.165.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2011/2011165/2011.165.00/syslog -startEsecs 1308088556.1339 -surveyName Dorado389_2011_165_00_165_00 >> ../results/2011165_GulperTimes.txt Executing: removeGulpDups.py ../results/2011165_GulperTimes.txt Bottle: 0 Time: 1308089961 Depth: 7.0182 Dist: 1.4079 Bottle: 3 Time: 1308093130 Depth: 1.6023 Dist: 4.5036 Bottle: 4 Time: 1308093681 Depth: 3.9636 Dist: 5.0519 Bottle: 5 Time: 1308097281 Depth: 23.0156 Dist: 8.6491 Bottle: 6 Time: 1308100881 Depth: 9.8326 Dist: 12.2675 Bottle: 1 Time: 1308106382 Depth: 3.016 Dist: 17.841 Bottle: 2 Time: 1308110812 Depth: 4.0811 Dist: 22.4421 Bottle: 7 Time: 1308121083 Depth: 24.3472 Dist: 32.9349 Bottle: 8 Time: 1308128284 Depth: 13.4543 Dist: 39.5403 Bottle: 9 Time: 1308135484 Depth: 5.6012 Dist: 46.6872 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_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_2011_165_00_165_00_2column.png Elapsed time to save image: 10 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_2011_165_00_165_00_biolume.png Elapsed time to save image: 40 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_2011_165_00_165_00_lopc.png Elapsed time to save image: 9 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_2column.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2011/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_2011_165_00_165_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_165_00_165_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_165_00_165_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_165_00_165_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_165_00_165_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_165_00_165_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_165_00_165_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_165_00_165_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_165_00_165_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_165_00_165_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_165_00_165_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_165_00_165_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_165_00_165_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_165_00_165_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_165_00_165_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_165_00_165_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_165_00_165_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_165_00_165_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2011_165_00_165_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00.kml... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_165_00_165_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_2011_165_00_165_00.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 19 NaNs found in bbpBlue. Interpolating anyway. 59 NaNs found in bbpRed. Interpolating anyway. 2 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 7131 NaN values in array of lon that is 64522 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 57391 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 57391 are not equal to number of Lat lon points = 64522 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_2011_165_00_165_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00.txt... Copied to /mbari/AUVCTD/surveys/2011/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2011/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... 19 NaNs found in bbpBlue. Interpolating anyway. 59 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_2011_165_00_165_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2011/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_2011_165_00_165_00.nc... Copied to /mbari/AUVCTD/surveys/2011/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2011/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_165_00_165_00.mat... Copied to /mbari/AUVCTD/surveys/2011/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2011_165_00_165_00 processed" mccann@mbari.org < mail_Dorado389_2011_165_00_165_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011.165.00.mat Processing time: 384 seconds