Execution of AUVprocess_main version 1.86 at 2018-05-24T20:43:23Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2013, ['297.01'], '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: 2013.297.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/ 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/2013/2013297/2013.297.01/navigation.nc') Creating vector time with 50331 elements. Creating vector mPos_x with 50331 elements. Creating vector time with 50331 elements. Creating vector mPos_y with 50331 elements. Creating vector time with 50331 elements. Creating vector mDepth with 50331 elements. Creating vector time with 50331 elements. Creating vector mGpsNorth with 50331 elements. Creating vector time with 50331 elements. Creating vector mGpsEast with 50331 elements. Creating vector time with 50331 elements. Creating vector mGpsValid with 50331 elements. Creating vector time with 50331 elements. Creating vector mPhi with 50331 elements. Creating vector time with 50331 elements. Creating vector mTheta with 50331 elements. Creating vector time with 50331 elements. Creating vector mPsi with 50331 elements. Creating vector time with 50331 elements. Creating vector mOmega_x with 50331 elements. Creating vector time with 50331 elements. Creating vector mOmega_y with 50331 elements. Creating vector time with 50331 elements. Creating vector mOmega_z with 50331 elements. Creating vector time with 50331 elements. Creating vector mPsaRange with 50331 elements. Creating vector time with 50331 elements. Creating vector mAltitude with 50331 elements. Creating vector time with 50331 elements. Creating vector mDvlAltitude with 50331 elements. Creating vector time with 50331 elements. Creating vector mEchoAltitude with 50331 elements. Creating vector time with 50331 elements. Creating vector mEchoHorizRange with 50331 elements. Creating vector time with 50331 elements. Creating vector mEchoAltitudeLast with 50331 elements. Creating vector time with 50331 elements. Creating vector mEchoHorizRangeLast with 50331 elements. Creating vector time with 50331 elements. Creating vector mEchoNumOfPings with 50331 elements. Creating vector time with 50331 elements. Creating vector mWaterSpeed with 50331 elements. Creating vector time with 50331 elements. Creating vector mDvlValid with 50331 elements. Creating vector time with 50331 elements. Creating vector mDvlNewData with 50331 elements. Creating vector time with 50331 elements. Creating vector mDeltaT with 50331 elements. Creating vector time with 50331 elements. Creating vector nfix with 50331 elements. Creating vector time with 50331 elements. Creating vector efix with 50331 elements. Creating vector time with 50331 elements. Creating vector filter_north with 50331 elements. Creating vector time with 50331 elements. Creating vector filter_east with 50331 elements. Creating vector time with 50331 elements. Creating vector filter_depth with 50331 elements. Creating vector time with 50331 elements. Creating vector north_current with 50331 elements. Creating vector time with 50331 elements. Creating vector east_current with 50331 elements. Creating vector time with 50331 elements. Creating vector speed_bias with 50331 elements. Creating vector time with 50331 elements. Creating vector heading_bias with 50331 elements. Creating vector time with 50331 elements. Creating vector latitude with 50331 elements. Creating vector time with 50331 elements. Creating vector longitude with 50331 elements. Creating vector time with 50331 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/navigation.nc'); processNav(): median of positive valued depths = 11.9721 processNav(): Finding depths less than 83.8044 and times > 0 processNav(): length(Nav.depth) = 50331 processNav(): length(gindx) = 50331 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/2013/2013297/2013.297.01/gps.nc') Creating vector time with 4013 elements. Creating vector hours with 4013 elements. Creating vector time with 4013 elements. Creating vector minutes with 4013 elements. Creating vector time with 4013 elements. Creating vector seconds with 4013 elements. Creating vector time with 4013 elements. Creating vector centiSeconds with 4013 elements. Creating vector time with 4013 elements. Creating vector latitude with 4013 elements. Creating vector time with 4013 elements. Creating vector longitude with 4013 elements. Creating vector time with 4013 elements. Creating vector quality with 4013 elements. Creating vector time with 4013 elements. Creating vector numberOfSatellites with 4013 elements. Creating vector time with 4013 elements. Creating vector hdop with 4013 elements. Creating vector time with 4013 elements. Creating vector antennaHeight with 4013 elements. Creating vector time with 4013 elements. Creating vector geoHeight with 4013 elements. Creating vector time with 4013 elements. Creating vector dgpsDataAge with 4013 elements. Creating vector time with 4013 elements. Creating vector dgpsRSID with 4013 elements. Creating vector time with 4013 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/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/2013/2013297/2013.297.01/parosci.nc') Creating vector time with 99391 elements. Creating vector depth with 99391 elements. Creating vector time with 99391 elements. Creating vector temp with 99391 elements. Creating vector time with 99391 elements. Creating vector pressure with 99391 elements. Creating vector time with 99391 elements. Creating vector temp_period with 99391 elements. Creating vector time with 99391 elements. Creating vector pres_period with 99391 elements. Creating vector time with 99391 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.1681 max(Depth.data) = 33.5127 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.1681 max(Depth.data) = 33.5127 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/2013/2013297/2013.297.01/hydroscatlog.nc') Creating vector time with 40364 elements. Creating vector Seconds with 40364 elements. Creating vector time with 40364 elements. Creating vector HundrethsOfSeconds with 40364 elements. Creating vector time with 40364 elements. Creating vector Snorm1 with 40364 elements. Creating vector time with 40364 elements. Creating vector Snorm2 with 40364 elements. Creating vector time with 40364 elements. Creating vector Snorm3 with 40364 elements. Creating vector time with 40364 elements. Creating vector Gain_Status_1 with 40364 elements. Creating vector time with 40364 elements. Creating vector Gain_Status_2 with 40364 elements. Creating vector time with 40364 elements. Creating vector Gain_Status_3 with 40364 elements. Creating vector time with 40364 elements. Creating vector RawDepthValue with 40364 elements. Creating vector time with 40364 elements. Creating vector RawTempValue with 40364 elements. Creating vector time with 40364 elements. Creating vector Temperature with 40364 elements. Creating vector time with 40364 elements. Creating vector ErrorValue with 40364 elements. Creating vector time with 40364 elements. Creating vector bb470 with 40364 elements. Creating vector time with 40364 elements. Creating vector bb676 with 40364 elements. Creating vector time with 40364 elements. Creating vector fl676u with 40364 elements. Creating vector time with 40364 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/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/2013/2013297/2013.297.01/ctdDriver.nc') Creating vector time with 40342 elements. Creating vector conductivity with 40342 elements. Creating vector time with 40342 elements. Creating vector temperature with 40342 elements. Creating vector time with 40342 elements. Creating vector cond_frequency with 40342 elements. Creating vector time with 40342 elements. Creating vector temp_frequency with 40342 elements. Creating vector time with 40342 elements. Creating vector spare with 40342 elements. Creating vector time with 40342 elements. Creating vector humidity with 40342 elements. Creating vector time with 40342 elements. Creating vector flow1 with 40342 elements. Creating vector time with 40342 elements. Creating vector CDOM with 40342 elements. Creating vector time with 40342 elements. Creating vector dissolvedO2 with 40342 elements. Creating vector time with 40342 elements. Creating vector salinity with 40342 elements. Creating vector time with 40342 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/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/2013/2013297/2013.297.01/ctdDriver2.nc') Creating vector time with 40343 elements. Creating vector conductivity with 40343 elements. Creating vector time with 40343 elements. Creating vector temperature with 40343 elements. Creating vector time with 40343 elements. Creating vector cond_frequency with 40343 elements. Creating vector time with 40343 elements. Creating vector temp_frequency with 40343 elements. Creating vector time with 40343 elements. Creating vector flow2 with 40343 elements. Creating vector time with 40343 elements. Creating vector spare with 40343 elements. Creating vector time with 40343 elements. Creating vector salinity with 40343 elements. Creating vector time with 40343 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/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/2013/2013297/2013.297.01/isuslog.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/isuslog.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/isuslog.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/isuslog.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting ISUS structure to NaN values. 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/2013/2013297/2013.297.01/biolume.nc') Creating vector time with 9935 elements. Creating vector rrr with 9935 elements. Creating vector time with 9935 elements. Creating vector cal_striing with 9935 elements. Creating vector time with 9935 elements. Creating vector avg_biolume with 9935 elements. Creating vector time with 9935 elements. Creating vector pump with 9935 elements. Creating vector time with 9935 elements. Creating vector system_voltage with 9935 elements. Creating vector time with 9935 elements. Creating vector flow with 9935 elements. Creating vector time with 9935 elements. Creating vector HV with 9935 elements. Creating vector time with 9935 elements. Creating vector reserved with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_0 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_1 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_2 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_3 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_4 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_5 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_6 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_7 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_8 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_9 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_10 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_11 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_12 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_13 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_14 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_15 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_16 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_17 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_18 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_19 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_20 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_21 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_22 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_23 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_24 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_25 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_26 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_27 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_28 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_29 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_30 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_31 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_32 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_33 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_34 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_35 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_36 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_37 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_38 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_39 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_40 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_41 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_42 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_43 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_44 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_45 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_46 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_47 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_48 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_49 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_50 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_51 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_52 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_53 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_54 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_55 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_56 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_57 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_58 with 9935 elements. Creating vector time with 9935 elements. Creating vector raw_59 with 9935 elements. Creating vector time with 9935 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/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/2013/2013297/2013.297.01/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (950 x 994) with 944300 elements. Creating vector time with 950 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (950 x 994) with 944300 elements. Creating vector time with 950 elements. Creating vector bin with 994 elements. Creating matrix countList (950 x 994) with 944300 elements. Creating vector time with 950 elements. Creating vector bin with 994 elements. Creating vector LCcount with 950 elements. Creating vector time with 950 elements. Creating vector transCount with 950 elements. Creating vector time with 950 elements. Creating vector nonTransCount with 950 elements. Creating vector time with 950 elements. Creating vector ai_mean with 950 elements. Creating vector time with 950 elements. Creating vector ai_min with 950 elements. Creating vector time with 950 elements. Creating vector ai_max with 950 elements. Creating vector time with 950 elements. Creating vector ai_std with 950 elements. Creating vector time with 950 elements. Creating vector esd_mean with 950 elements. Creating vector time with 950 elements. Creating vector esd_min with 950 elements. Creating vector time with 950 elements. Creating vector esd_max with 950 elements. Creating vector time with 950 elements. Creating vector esd_std with 950 elements. Creating vector time with 950 elements. Creating vector countSum with 950 elements. Creating vector time with 950 elements. Creating vector snapshot with 950 elements. Creating vector time with 950 elements. Creating vector threshold with 950 elements. Creating vector time with 950 elements. Creating vector sampleCount with 950 elements. Creating vector time with 950 elements. Creating vector flowCount with 950 elements. Creating vector time with 950 elements. Creating vector flowTime with 950 elements. Creating vector time with 950 elements. Creating vector bufferStatus with 950 elements. Creating vector time with 950 elements. Creating vector laserLevel with 950 elements. Creating vector time with 950 elements. Creating vector counter with 950 elements. Creating vector time with 950 elements. Creating vector counterPeriod with 950 elements. Creating vector time with 950 elements. Creating vector laserControl with 950 elements. Creating vector time with 950 elements. Creating vector countUnknownFrameCharacter with 950 elements. Creating vector time with 950 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 950 elements. Creating vector time with 950 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 950 elements. Creating vector time with 950 elements. Creating vector flowSpeed with 950 elements. Creating vector time with 950 elements. Creating vector countShortLFrameError with 950 elements. Creating vector time with 950 elements. Creating vector countGarbledLFrame with 950 elements. Creating vector time with 950 elements. Creating vector cFrameEsecs with 950 elements. Creating vector time with 950 elements. Creating vector correctedSampleCountList with 950 elements. Creating vector time with 950 elements. Creating vector time with 950 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013297/2013.297.01/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.297.01.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_2013.297.01.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_297_01_297_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_297_01_297_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_297_01_297_01.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 = 64 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 Only one good point - NaNing the gN array. BL BLflow LOPC count transCount nonTransCount LCcount Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN No valid data for 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 31694 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 31694 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 118898 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 10/24/2013 05:30 to 10/24/2013 10:29 swr = 1.4377 1.4621 3.8652 17.7496 45.0987 72.9171 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_297_01_297_01_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2013297_GulperTimes.txt && touch ../results/2013297_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/2013/2013297/2013.297.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013297/2013.297.01/syslog -startEsecs 1382625199.0654 -surveyName Dorado389_2013_297_01_297_01 >> ../results/2013297_GulperTimes.txt Executing: removeGulpDups.py ../results/2013297_GulperTimes.txt Bottle: 0 Time: 1382626309 Depth: 3.2726 Dist: 1.3541 Bottle: 1 Time: 1382626785 Depth: 1.9977 Dist: 2.0013 Bottle: 2 Time: 1382627436 Depth: 4.2893 Dist: 2.831 Bottle: 3 Time: 1382627857 Depth: 3.6479 Dist: 3.4195 Bottle: 4 Time: 1382628736 Depth: 1.8398 Dist: 4.6476 Bottle: 5 Time: 1382629483 Depth: 3.0492 Dist: 5.6247 Bottle: 6 Time: 1382629972 Depth: 5.1054 Dist: 6.3087 Bottle: 7 Time: 1382630671 Depth: 0.38125 Dist: 7.2544 Bottle: 8 Time: 1382631282 Depth: 10.9584 Dist: 8.0304 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_297_01_297_01_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_297_01_297_01_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_297_01_297_01_biolume.png Elapsed time to save image: 28 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_297_01_297_01_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_297_01_297_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_297_01_297_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_297_01_297_01_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_297_01_297_01_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_297_01_297_01_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_297_01_297_01_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_297_01_297_01_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_297_01_297_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_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); length(v_esecs(gindx)) = which is less than 2. Not processing. updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_Chlorophyll_Fluorescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_Bioluminescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_LOPC_Total_Count.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_297_01_297_01_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_297_01_297_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_297_01_297_01.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_297_01_297_01_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_297_01_297_01.mat ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Encountered 866 NaN values in array of lon that is 4035 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 3169 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 3169 are not equal to number of Lat lon points = 4035 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_297_01_297_01.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_297_01_297_01_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_297_01_297_01.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_297_01_297_01_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... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_297_01_297_01_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_297_01_297_01.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_297_01_297_01_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_297_01_297_01.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_297_01_297_01 processed" mccann@mbari.org < mail_Dorado389_2013_297_01_297_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.297.01.mat Processing time: 56 seconds