Execution of AUVprocess_main version 1.86 at 2018-05-24T19:43:05Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2013, ['262.00'], '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: 2013.262.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/ 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/2013/2013262/2013.262.00/navigation.nc') Creating vector time with 35210 elements. Creating vector mPos_x with 35210 elements. Creating vector time with 35210 elements. Creating vector mPos_y with 35210 elements. Creating vector time with 35210 elements. Creating vector mDepth with 35210 elements. Creating vector time with 35210 elements. Creating vector mGpsNorth with 35210 elements. Creating vector time with 35210 elements. Creating vector mGpsEast with 35210 elements. Creating vector time with 35210 elements. Creating vector mGpsValid with 35210 elements. Creating vector time with 35210 elements. Creating vector mPhi with 35210 elements. Creating vector time with 35210 elements. Creating vector mTheta with 35210 elements. Creating vector time with 35210 elements. Creating vector mPsi with 35210 elements. Creating vector time with 35210 elements. Creating vector mOmega_x with 35210 elements. Creating vector time with 35210 elements. Creating vector mOmega_y with 35210 elements. Creating vector time with 35210 elements. Creating vector mOmega_z with 35210 elements. Creating vector time with 35210 elements. Creating vector mPsaRange with 35210 elements. Creating vector time with 35210 elements. Creating vector mAltitude with 35210 elements. Creating vector time with 35210 elements. Creating vector mDvlAltitude with 35210 elements. Creating vector time with 35210 elements. Creating vector mEchoAltitude with 35210 elements. Creating vector time with 35210 elements. Creating vector mEchoHorizRange with 35210 elements. Creating vector time with 35210 elements. Creating vector mEchoAltitudeLast with 35210 elements. Creating vector time with 35210 elements. Creating vector mEchoHorizRangeLast with 35210 elements. Creating vector time with 35210 elements. Creating vector mEchoNumOfPings with 35210 elements. Creating vector time with 35210 elements. Creating vector mWaterSpeed with 35210 elements. Creating vector time with 35210 elements. Creating vector mDvlValid with 35210 elements. Creating vector time with 35210 elements. Creating vector mDvlNewData with 35210 elements. Creating vector time with 35210 elements. Creating vector mDeltaT with 35210 elements. Creating vector time with 35210 elements. Creating vector nfix with 35210 elements. Creating vector time with 35210 elements. Creating vector efix with 35210 elements. Creating vector time with 35210 elements. Creating vector filter_north with 35210 elements. Creating vector time with 35210 elements. Creating vector filter_east with 35210 elements. Creating vector time with 35210 elements. Creating vector filter_depth with 35210 elements. Creating vector time with 35210 elements. Creating vector north_current with 35210 elements. Creating vector time with 35210 elements. Creating vector east_current with 35210 elements. Creating vector time with 35210 elements. Creating vector speed_bias with 35210 elements. Creating vector time with 35210 elements. Creating vector heading_bias with 35210 elements. Creating vector time with 35210 elements. Creating vector latitude with 35210 elements. Creating vector time with 35210 elements. Creating vector longitude with 35210 elements. Creating vector time with 35210 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/navigation.nc'); processNav(): median of positive valued depths = 13.7594 processNav(): Finding depths less than 96.3156 and times > 0 processNav(): length(Nav.depth) = 35210 processNav(): length(gindx) = 35210 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/2013/2013262/2013.262.00/gps.nc') Creating vector time with 786 elements. Creating vector hours with 786 elements. Creating vector time with 786 elements. Creating vector minutes with 786 elements. Creating vector time with 786 elements. Creating vector seconds with 786 elements. Creating vector time with 786 elements. Creating vector centiSeconds with 786 elements. Creating vector time with 786 elements. Creating vector latitude with 786 elements. Creating vector time with 786 elements. Creating vector longitude with 786 elements. Creating vector time with 786 elements. Creating vector quality with 786 elements. Creating vector time with 786 elements. Creating vector numberOfSatellites with 786 elements. Creating vector time with 786 elements. Creating vector hdop with 786 elements. Creating vector time with 786 elements. Creating vector antennaHeight with 786 elements. Creating vector time with 786 elements. Creating vector geoHeight with 786 elements. Creating vector time with 786 elements. Creating vector dgpsDataAge with 786 elements. Creating vector time with 786 elements. Creating vector dgpsRSID with 786 elements. Creating vector time with 786 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/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/2013/2013262/2013.262.00/parosci.nc') Creating vector time with 69606 elements. Creating vector depth with 69606 elements. Creating vector time with 69606 elements. Creating vector temp with 69606 elements. Creating vector time with 69606 elements. Creating vector pressure with 69606 elements. Creating vector time with 69606 elements. Creating vector temp_period with 69606 elements. Creating vector time with 69606 elements. Creating vector pres_period with 69606 elements. Creating vector time with 69606 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.21392 max(Depth.data) = 35.2384 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.21392 max(Depth.data) = 35.2384 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/2013/2013262/2013.262.00/hydroscatlog.nc') Creating vector time with 28257 elements. Creating vector Seconds with 28257 elements. Creating vector time with 28257 elements. Creating vector HundrethsOfSeconds with 28257 elements. Creating vector time with 28257 elements. Creating vector Snorm1 with 28257 elements. Creating vector time with 28257 elements. Creating vector Snorm2 with 28257 elements. Creating vector time with 28257 elements. Creating vector Snorm3 with 28257 elements. Creating vector time with 28257 elements. Creating vector Gain_Status_1 with 28257 elements. Creating vector time with 28257 elements. Creating vector Gain_Status_2 with 28257 elements. Creating vector time with 28257 elements. Creating vector Gain_Status_3 with 28257 elements. Creating vector time with 28257 elements. Creating vector RawDepthValue with 28257 elements. Creating vector time with 28257 elements. Creating vector RawTempValue with 28257 elements. Creating vector time with 28257 elements. Creating vector Temperature with 28257 elements. Creating vector time with 28257 elements. Creating vector ErrorValue with 28257 elements. Creating vector time with 28257 elements. Creating vector bb470 with 28257 elements. Creating vector time with 28257 elements. Creating vector bb676 with 28257 elements. Creating vector time with 28257 elements. Creating vector fl676u with 28257 elements. Creating vector time with 28257 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/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/2013/2013262/2013.262.00/ctdDriver.nc') Creating vector time with 28207 elements. Creating vector conductivity with 28207 elements. Creating vector time with 28207 elements. Creating vector temperature with 28207 elements. Creating vector time with 28207 elements. Creating vector cond_frequency with 28207 elements. Creating vector time with 28207 elements. Creating vector temp_frequency with 28207 elements. Creating vector time with 28207 elements. Creating vector spare with 28207 elements. Creating vector time with 28207 elements. Creating vector humidity with 28207 elements. Creating vector time with 28207 elements. Creating vector flow1 with 28207 elements. Creating vector time with 28207 elements. Creating vector CDOM with 28207 elements. Creating vector time with 28207 elements. Creating vector dissolvedO2 with 28207 elements. Creating vector time with 28207 elements. Creating vector salinity with 28207 elements. Creating vector time with 28207 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/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/2013/2013262/2013.262.00/ctdDriver2.nc') Creating vector time with 28203 elements. Creating vector conductivity with 28203 elements. Creating vector time with 28203 elements. Creating vector temperature with 28203 elements. Creating vector time with 28203 elements. Creating vector cond_frequency with 28203 elements. Creating vector time with 28203 elements. Creating vector temp_frequency with 28203 elements. Creating vector time with 28203 elements. Creating vector flow2 with 28203 elements. Creating vector time with 28203 elements. Creating vector spare with 28203 elements. Creating vector time with 28203 elements. Creating vector salinity with 28203 elements. Creating vector time with 28203 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/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/2013/2013262/2013.262.00/isuslog.nc') Creating vector time with 6649 elements. Creating vector isusNitrate with 6649 elements. Creating vector time with 6649 elements. Creating vector isusTemp with 6649 elements. Creating vector time with 6649 elements. Creating vector isusQuality with 6649 elements. Creating vector time with 6649 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/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/2013/2013262/2013.262.00/biolume.nc') Creating vector time with 6959 elements. Creating vector rrr with 6959 elements. Creating vector time with 6959 elements. Creating vector cal_striing with 6959 elements. Creating vector time with 6959 elements. Creating vector avg_biolume with 6959 elements. Creating vector time with 6959 elements. Creating vector pump with 6959 elements. Creating vector time with 6959 elements. Creating vector system_voltage with 6959 elements. Creating vector time with 6959 elements. Creating vector flow with 6959 elements. Creating vector time with 6959 elements. Creating vector HV with 6959 elements. Creating vector time with 6959 elements. Creating vector reserved with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_0 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_1 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_2 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_3 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_4 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_5 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_6 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_7 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_8 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_9 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_10 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_11 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_12 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_13 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_14 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_15 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_16 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_17 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_18 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_19 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_20 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_21 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_22 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_23 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_24 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_25 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_26 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_27 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_28 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_29 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_30 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_31 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_32 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_33 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_34 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_35 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_36 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_37 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_38 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_39 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_40 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_41 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_42 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_43 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_44 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_45 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_46 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_47 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_48 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_49 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_50 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_51 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_52 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_53 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_54 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_55 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_56 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_57 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_58 with 6959 elements. Creating vector time with 6959 elements. Creating vector raw_59 with 6959 elements. Creating vector time with 6959 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/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/2013/2013262/2013.262.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (661 x 994) with 657034 elements. Creating vector time with 661 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (661 x 994) with 657034 elements. Creating vector time with 661 elements. Creating vector bin with 994 elements. Creating matrix countList (661 x 994) with 657034 elements. Creating vector time with 661 elements. Creating vector bin with 994 elements. Creating vector LCcount with 661 elements. Creating vector time with 661 elements. Creating vector transCount with 661 elements. Creating vector time with 661 elements. Creating vector nonTransCount with 661 elements. Creating vector time with 661 elements. Creating vector ai_mean with 661 elements. Creating vector time with 661 elements. Creating vector ai_min with 661 elements. Creating vector time with 661 elements. Creating vector ai_max with 661 elements. Creating vector time with 661 elements. Creating vector ai_std with 661 elements. Creating vector time with 661 elements. Creating vector esd_mean with 661 elements. Creating vector time with 661 elements. Creating vector esd_min with 661 elements. Creating vector time with 661 elements. Creating vector esd_max with 661 elements. Creating vector time with 661 elements. Creating vector esd_std with 661 elements. Creating vector time with 661 elements. Creating vector countSum with 661 elements. Creating vector time with 661 elements. Creating vector snapshot with 661 elements. Creating vector time with 661 elements. Creating vector threshold with 661 elements. Creating vector time with 661 elements. Creating vector sampleCount with 661 elements. Creating vector time with 661 elements. Creating vector flowCount with 661 elements. Creating vector time with 661 elements. Creating vector flowTime with 661 elements. Creating vector time with 661 elements. Creating vector bufferStatus with 661 elements. Creating vector time with 661 elements. Creating vector laserLevel with 661 elements. Creating vector time with 661 elements. Creating vector counter with 661 elements. Creating vector time with 661 elements. Creating vector counterPeriod with 661 elements. Creating vector time with 661 elements. Creating vector laserControl with 661 elements. Creating vector time with 661 elements. Creating vector countUnknownFrameCharacter with 661 elements. Creating vector time with 661 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 661 elements. Creating vector time with 661 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 661 elements. Creating vector time with 661 elements. Creating vector flowSpeed with 661 elements. Creating vector time with 661 elements. Creating vector countShortLFrameError with 661 elements. Creating vector time with 661 elements. Creating vector countGarbledLFrame with 661 elements. Creating vector time with 661 elements. Creating vector cFrameEsecs with 661 elements. Creating vector time with 661 elements. Creating vector correctedSampleCountList with 661 elements. Creating vector time with 661 elements. Creating vector time with 661 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013262/2013.262.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.262.00.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_2013.262.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 3 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_262_00_262_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_262_00_262_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_262_00_262_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 = 84 Gridding with nix = 252, iZ = 67 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 Only one good point or fewer - NaNing the gLOPCcount array. - NaNing the gLOPCtransCount array. - NaNing the gLOPCnonTransCount array. - NaNing the gLOPCLCcount array. 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 No valid data for gLOPCcount cvarname = gLOPCtransCount No valid data for gLOPCtransCount cvarname = gLOPCnonTransCount No valid data for gLOPCnonTransCount cvarname = gLOPCLCcount No valid data for gLOPCLCcount Encountered 0 NaN values in array of lon that is 29274 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 29274 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: 09/19/2013 05:30 to 09/19/2013 09:30 swr = 1.7050 2.5503 46.7339 266.9652 465.4861 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_262_00_262_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2013262_GulperTimes.txt && touch ../results/2013262_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/2013/2013262/2013.262.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013262/2013.262.00/syslog -startEsecs 1379601672.1989 -surveyName Dorado389_2013_262_00_262_00 >> ../results/2013262_GulperTimes.txt Executing: removeGulpDups.py ../results/2013262_GulperTimes.txt Bottle: 0 Time: 1379603023 Depth: 2.6234 Dist: 1.7122 Bottle: 1 Time: 1379603541 Depth: 2.7555 Dist: 2.3975 Bottle: 2 Time: 1379604227 Depth: 2.539 Dist: 3.1968 Bottle: 3 Time: 1379604834 Depth: 3.0275 Dist: 4.0229 Bottle: 4 Time: 1379605473 Depth: 2.5728 Dist: 4.9098 Bottle: 5 Time: 1379606073 Depth: 2.6879 Dist: 5.6507 Bottle: 6 Time: 1379606573 Depth: 4.3173 Dist: 6.3361 Bottle: 7 Time: 1379607293 Depth: 3.4098 Dist: 7.341 Bottle 8 time is 234.2222 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_262_00_262_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_2013_262_00_262_00_2column.png Elapsed time to save image: 7 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_2013_262_00_262_00_biolume.png Elapsed time to save image: 26 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_262_00_262_00_lopc.png Elapsed time to save image: 7 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_262_00_262_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_262_00_262_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_262_00_262_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_262_00_262_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_262_00_262_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_262_00_262_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_262_00_262_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_262_00_262_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_262_00_262_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_262_00_262_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_262_00_262_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_262_00_262_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_262_00_262_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_262_00_262_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_262_00_262_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_262_00_262_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_262_00_262_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_262_00_262_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_262_00_262_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_262_00_262_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_262_00_262_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_262_00_262_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_262_00_262_00_Bioluminescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_262_00_262_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); Could not create .kmz for LOPC Total Count Creating Dorado389_2013_262_00_262_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_262_00_262_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_262_00_262_00_Bioluminescence.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_262_00_262_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in bbpBlue. Interpolating anyway. Encountered 1092 NaN values in array of lon that is 6405 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 5313 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 5313 are not equal to number of Lat lon points = 6405 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_2013_262_00_262_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_262_00_262_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_262_00_262_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_262_00_262_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 isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in bbpBlue. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_262_00_262_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_262_00_262_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_262_00_262_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_262_00_262_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_262_00_262_00 processed" mccann@mbari.org < mail_Dorado389_2013_262_00_262_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.262.00.mat Processing time: 52 seconds