Execution of AUVprocess_main version 1.86 at 2018-05-24T17:33:01Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2013, ['227.01'], '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: 2013.227.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/ 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/2013/2013227/2013.227.01/navigation.nc') Creating vector time with 63835 elements. Creating vector mPos_x with 63835 elements. Creating vector time with 63835 elements. Creating vector mPos_y with 63835 elements. Creating vector time with 63835 elements. Creating vector mDepth with 63835 elements. Creating vector time with 63835 elements. Creating vector mGpsNorth with 63835 elements. Creating vector time with 63835 elements. Creating vector mGpsEast with 63835 elements. Creating vector time with 63835 elements. Creating vector mGpsValid with 63835 elements. Creating vector time with 63835 elements. Creating vector mPhi with 63835 elements. Creating vector time with 63835 elements. Creating vector mTheta with 63835 elements. Creating vector time with 63835 elements. Creating vector mPsi with 63835 elements. Creating vector time with 63835 elements. Creating vector mOmega_x with 63835 elements. Creating vector time with 63835 elements. Creating vector mOmega_y with 63835 elements. Creating vector time with 63835 elements. Creating vector mOmega_z with 63835 elements. Creating vector time with 63835 elements. Creating vector mPsaRange with 63835 elements. Creating vector time with 63835 elements. Creating vector mAltitude with 63835 elements. Creating vector time with 63835 elements. Creating vector mDvlAltitude with 63835 elements. Creating vector time with 63835 elements. Creating vector mEchoAltitude with 63835 elements. Creating vector time with 63835 elements. Creating vector mEchoHorizRange with 63835 elements. Creating vector time with 63835 elements. Creating vector mEchoAltitudeLast with 63835 elements. Creating vector time with 63835 elements. Creating vector mEchoHorizRangeLast with 63835 elements. Creating vector time with 63835 elements. Creating vector mEchoNumOfPings with 63835 elements. Creating vector time with 63835 elements. Creating vector mWaterSpeed with 63835 elements. Creating vector time with 63835 elements. Creating vector mDvlValid with 63835 elements. Creating vector time with 63835 elements. Creating vector mDvlNewData with 63835 elements. Creating vector time with 63835 elements. Creating vector mDeltaT with 63835 elements. Creating vector time with 63835 elements. Creating vector nfix with 63835 elements. Creating vector time with 63835 elements. Creating vector efix with 63835 elements. Creating vector time with 63835 elements. Creating vector filter_north with 63835 elements. Creating vector time with 63835 elements. Creating vector filter_east with 63835 elements. Creating vector time with 63835 elements. Creating vector filter_depth with 63835 elements. Creating vector time with 63835 elements. Creating vector north_current with 63835 elements. Creating vector time with 63835 elements. Creating vector east_current with 63835 elements. Creating vector time with 63835 elements. Creating vector speed_bias with 63835 elements. Creating vector time with 63835 elements. Creating vector heading_bias with 63835 elements. Creating vector time with 63835 elements. Creating vector latitude with 63835 elements. Creating vector time with 63835 elements. Creating vector longitude with 63835 elements. Creating vector time with 63835 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/navigation.nc'); processNav(): median of positive valued depths = 20.1327 processNav(): Finding depths less than 140.9288 and times > 0 processNav(): length(Nav.depth) = 63835 processNav(): length(gindx) = 63835 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/2013/2013227/2013.227.01/gps.nc') Creating vector time with 616 elements. Creating vector hours with 616 elements. Creating vector time with 616 elements. Creating vector minutes with 616 elements. Creating vector time with 616 elements. Creating vector seconds with 616 elements. Creating vector time with 616 elements. Creating vector centiSeconds with 616 elements. Creating vector time with 616 elements. Creating vector latitude with 616 elements. Creating vector time with 616 elements. Creating vector longitude with 616 elements. Creating vector time with 616 elements. Creating vector quality with 616 elements. Creating vector time with 616 elements. Creating vector numberOfSatellites with 616 elements. Creating vector time with 616 elements. Creating vector hdop with 616 elements. Creating vector time with 616 elements. Creating vector antennaHeight with 616 elements. Creating vector time with 616 elements. Creating vector geoHeight with 616 elements. Creating vector time with 616 elements. Creating vector dgpsDataAge with 616 elements. Creating vector time with 616 elements. Creating vector dgpsRSID with 616 elements. Creating vector time with 616 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/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/2013/2013227/2013.227.01/parosci.nc') Creating vector time with 125723 elements. Creating vector depth with 125723 elements. Creating vector time with 125723 elements. Creating vector temp with 125723 elements. Creating vector time with 125723 elements. Creating vector pressure with 125723 elements. Creating vector time with 125723 elements. Creating vector temp_period with 125723 elements. Creating vector time with 125723 elements. Creating vector pres_period with 125723 elements. Creating vector time with 125723 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.30504 max(Depth.data) = 80.6017 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.30504 max(Depth.data) = 80.6017 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/2013/2013227/2013.227.01/hydroscatlog.nc') Creating vector time with 51153 elements. Creating vector Seconds with 51153 elements. Creating vector time with 51153 elements. Creating vector HundrethsOfSeconds with 51153 elements. Creating vector time with 51153 elements. Creating vector Snorm1 with 51153 elements. Creating vector time with 51153 elements. Creating vector Snorm2 with 51153 elements. Creating vector time with 51153 elements. Creating vector Snorm3 with 51153 elements. Creating vector time with 51153 elements. Creating vector Gain_Status_1 with 51153 elements. Creating vector time with 51153 elements. Creating vector Gain_Status_2 with 51153 elements. Creating vector time with 51153 elements. Creating vector Gain_Status_3 with 51153 elements. Creating vector time with 51153 elements. Creating vector RawDepthValue with 51153 elements. Creating vector time with 51153 elements. Creating vector RawTempValue with 51153 elements. Creating vector time with 51153 elements. Creating vector Temperature with 51153 elements. Creating vector time with 51153 elements. Creating vector ErrorValue with 51153 elements. Creating vector time with 51153 elements. Creating vector bb470 with 51153 elements. Creating vector time with 51153 elements. Creating vector bb676 with 51153 elements. Creating vector time with 51153 elements. Creating vector fl676u with 51153 elements. Creating vector time with 51153 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/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/2013/2013227/2013.227.01/ctdDriver.nc') Creating vector time with 50969 elements. Creating vector conductivity with 50969 elements. Creating vector time with 50969 elements. Creating vector temperature with 50969 elements. Creating vector time with 50969 elements. Creating vector cond_frequency with 50969 elements. Creating vector time with 50969 elements. Creating vector temp_frequency with 50969 elements. Creating vector time with 50969 elements. Creating vector spare with 50969 elements. Creating vector time with 50969 elements. Creating vector humidity with 50969 elements. Creating vector time with 50969 elements. Creating vector flow1 with 50969 elements. Creating vector time with 50969 elements. Creating vector CDOM with 50969 elements. Creating vector time with 50969 elements. Creating vector dissolvedO2 with 50969 elements. Creating vector time with 50969 elements. Creating vector salinity with 50969 elements. Creating vector time with 50969 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/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/2013/2013227/2013.227.01/ctdDriver2.nc') Creating vector time with 51092 elements. Creating vector conductivity with 51092 elements. Creating vector time with 51092 elements. Creating vector temperature with 51092 elements. Creating vector time with 51092 elements. Creating vector cond_frequency with 51092 elements. Creating vector time with 51092 elements. Creating vector temp_frequency with 51092 elements. Creating vector time with 51092 elements. Creating vector flow2 with 51092 elements. Creating vector time with 51092 elements. Creating vector spare with 51092 elements. Creating vector time with 51092 elements. Creating vector salinity with 51092 elements. Creating vector time with 51092 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/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/2013/2013227/2013.227.01/isuslog.nc') Creating vector time with 11829 elements. Creating vector isusNitrate with 11829 elements. Creating vector time with 11829 elements. Creating vector isusTemp with 11829 elements. Creating vector time with 11829 elements. Creating vector isusQuality with 11829 elements. Creating vector time with 11829 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/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/2013/2013227/2013.227.01/biolume.nc') Creating vector time with 12587 elements. Creating vector rrr with 12587 elements. Creating vector time with 12587 elements. Creating vector cal_striing with 12587 elements. Creating vector time with 12587 elements. Creating vector avg_biolume with 12587 elements. Creating vector time with 12587 elements. Creating vector pump with 12587 elements. Creating vector time with 12587 elements. Creating vector system_voltage with 12587 elements. Creating vector time with 12587 elements. Creating vector flow with 12587 elements. Creating vector time with 12587 elements. Creating vector HV with 12587 elements. Creating vector time with 12587 elements. Creating vector reserved with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_0 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_1 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_2 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_3 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_4 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_5 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_6 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_7 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_8 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_9 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_10 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_11 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_12 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_13 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_14 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_15 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_16 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_17 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_18 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_19 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_20 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_21 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_22 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_23 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_24 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_25 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_26 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_27 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_28 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_29 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_30 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_31 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_32 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_33 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_34 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_35 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_36 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_37 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_38 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_39 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_40 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_41 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_42 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_43 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_44 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_45 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_46 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_47 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_48 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_49 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_50 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_51 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_52 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_53 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_54 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_55 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_56 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_57 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_58 with 12587 elements. Creating vector time with 12587 elements. Creating vector raw_59 with 12587 elements. Creating vector time with 12587 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/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/2013/2013227/2013.227.01/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (835 x 994) with 829990 elements. Creating vector time with 835 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (835 x 994) with 829990 elements. Creating vector time with 835 elements. Creating vector bin with 994 elements. Creating matrix countList (835 x 994) with 829990 elements. Creating vector time with 835 elements. Creating vector bin with 994 elements. Creating vector LCcount with 835 elements. Creating vector time with 835 elements. Creating vector transCount with 835 elements. Creating vector time with 835 elements. Creating vector nonTransCount with 835 elements. Creating vector time with 835 elements. Creating vector ai_mean with 835 elements. Creating vector time with 835 elements. Creating vector ai_min with 835 elements. Creating vector time with 835 elements. Creating vector ai_max with 835 elements. Creating vector time with 835 elements. Creating vector ai_std with 835 elements. Creating vector time with 835 elements. Creating vector esd_mean with 835 elements. Creating vector time with 835 elements. Creating vector esd_min with 835 elements. Creating vector time with 835 elements. Creating vector esd_max with 835 elements. Creating vector time with 835 elements. Creating vector esd_std with 835 elements. Creating vector time with 835 elements. Creating vector countSum with 835 elements. Creating vector time with 835 elements. Creating vector snapshot with 835 elements. Creating vector time with 835 elements. Creating vector threshold with 835 elements. Creating vector time with 835 elements. Creating vector sampleCount with 835 elements. Creating vector time with 835 elements. Creating vector flowCount with 835 elements. Creating vector time with 835 elements. Creating vector flowTime with 835 elements. Creating vector time with 835 elements. Creating vector bufferStatus with 835 elements. Creating vector time with 835 elements. Creating vector laserLevel with 835 elements. Creating vector time with 835 elements. Creating vector counter with 835 elements. Creating vector time with 835 elements. Creating vector counterPeriod with 835 elements. Creating vector time with 835 elements. Creating vector laserControl with 835 elements. Creating vector time with 835 elements. Creating vector countUnknownFrameCharacter with 835 elements. Creating vector time with 835 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 835 elements. Creating vector time with 835 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 835 elements. Creating vector time with 835 elements. Creating vector flowSpeed with 835 elements. Creating vector time with 835 elements. Creating vector countShortLFrameError with 835 elements. Creating vector time with 835 elements. Creating vector countGarbledLFrame with 835 elements. Creating vector time with 835 elements. Creating vector cFrameEsecs with 835 elements. Creating vector time with 835 elements. Creating vector correctedSampleCountList with 835 elements. Creating vector time with 835 elements. Creating vector time with 835 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013227/2013.227.01/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.227.01.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_2013.227.01.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 9 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_227_01_227_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_227_01_227_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_227_01_227_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 = 112 Gridding with nix = 336, iZ = 158 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 60346 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 60346 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 118895 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 08/15/2013 09:30 to 08/15/2013 15:30 swr = 522.5291 703.1002 855.5918 949.7978 921.9009 778.8171 771.1473 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_227_01_227_01_swr.png [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 564) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Done plotting SWR. Executing: /bin/rm -f ../results/2013227_GulperTimes.txt && touch ../results/2013227_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/2013/2013227/2013.227.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013227/2013.227.01/syslog -startEsecs 1376591502.0845 -surveyName Dorado389_2013_227_01_227_01 >> ../results/2013227_GulperTimes.txt Executing: removeGulpDups.py ../results/2013227_GulperTimes.txt Bottle: 0 Time: 1376597232 Depth: 8.8402 Dist: 8.0759 Bottle: 1 Time: 1376597668 Depth: 12.6895 Dist: 8.633 Bottle: 2 Time: 1376598140 Depth: 6.9955 Dist: 9.253 Bottle: 3 Time: 1376598553 Depth: 8.322 Dist: 9.8338 Bottle: 4 Time: 1376600021 Depth: 6.1784 Dist: 11.8978 Bottle: 5 Time: 1376600712 Depth: 6.8644 Dist: 12.8253 Bottle: 6 Time: 1376601502 Depth: 4.9631 Dist: 13.8271 Bottle: 7 Time: 1376601830 Depth: 4.7089 Dist: 14.2902 Bottle: 8 Time: 1376602233 Depth: 11.2479 Dist: 14.8533 Bottle: 9 Time: 1376602703 Depth: 8.3349 Dist: 15.3884 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_227_01_227_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_227_01_227_01_2column.png Elapsed time to save image: 9 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN 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_227_01_227_01_biolume.png Elapsed time to save image: 32 seconds 2Column contouring gridded variable gLOPCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCtransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCnonTransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCLCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_227_01_227_01_lopc.png Elapsed time to save image: 10 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_227_01_227_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_227_01_227_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_227_01_227_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_227_01_227_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_227_01_227_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_227_01_227_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_227_01_227_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_227_01_227_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_227_01_227_01_Temperature.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_227_01_227_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_227_01_227_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_227_01_227_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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_227_01_227_01_Nitrate.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_227_01_227_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_227_01_227_01_Oxygen.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_227_01_227_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_227_01_227_01_Optical_Backscatter_420_nm.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_227_01_227_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_227_01_227_01_Optical_Backscatter_700_nm.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_227_01_227_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_227_01_227_01_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_227_01_227_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_227_01_227_01_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_227_01_227_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_227_01_227_01_LOPC_Total_Count.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_227_01_227_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_227_01_227_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_227_01_227_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_227_01_227_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_227_01_227_01.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 43 NaNs found in bbpBlue. Interpolating anyway. 61 NaNs found in bbpRed. Interpolating anyway. 9 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 636 NaN values in array of lon that is 11623 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 10987 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 10987 are not equal to number of Lat lon points = 11623 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_227_01_227_01.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_227_01_227_01_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_227_01_227_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_227_01_227_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 isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 43 NaNs found in bbpBlue. Interpolating anyway. 61 NaNs found in bbpRed. Interpolating anyway. 9 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_2013_227_01_227_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_227_01_227_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_227_01_227_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_227_01_227_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_227_01_227_01 processed" mccann@mbari.org < mail_Dorado389_2013_227_01_227_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.227.01.mat Processing time: 169 seconds