Execution of AUVprocess_main version 1.86 at 2018-05-24T20:05:31Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2013, ['276.00'], '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: 2013.276.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/ 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/2013/2013276/2013.276.00/navigation.nc') Creating vector time with 113968 elements. Creating vector mPos_x with 113968 elements. Creating vector time with 113968 elements. Creating vector mPos_y with 113968 elements. Creating vector time with 113968 elements. Creating vector mDepth with 113968 elements. Creating vector time with 113968 elements. Creating vector mGpsNorth with 113968 elements. Creating vector time with 113968 elements. Creating vector mGpsEast with 113968 elements. Creating vector time with 113968 elements. Creating vector mGpsValid with 113968 elements. Creating vector time with 113968 elements. Creating vector mPhi with 113968 elements. Creating vector time with 113968 elements. Creating vector mTheta with 113968 elements. Creating vector time with 113968 elements. Creating vector mPsi with 113968 elements. Creating vector time with 113968 elements. Creating vector mOmega_x with 113968 elements. Creating vector time with 113968 elements. Creating vector mOmega_y with 113968 elements. Creating vector time with 113968 elements. Creating vector mOmega_z with 113968 elements. Creating vector time with 113968 elements. Creating vector mPsaRange with 113968 elements. Creating vector time with 113968 elements. Creating vector mAltitude with 113968 elements. Creating vector time with 113968 elements. Creating vector mDvlAltitude with 113968 elements. Creating vector time with 113968 elements. Creating vector mEchoAltitude with 113968 elements. Creating vector time with 113968 elements. Creating vector mEchoHorizRange with 113968 elements. Creating vector time with 113968 elements. Creating vector mEchoAltitudeLast with 113968 elements. Creating vector time with 113968 elements. Creating vector mEchoHorizRangeLast with 113968 elements. Creating vector time with 113968 elements. Creating vector mEchoNumOfPings with 113968 elements. Creating vector time with 113968 elements. Creating vector mWaterSpeed with 113968 elements. Creating vector time with 113968 elements. Creating vector mDvlValid with 113968 elements. Creating vector time with 113968 elements. Creating vector mDvlNewData with 113968 elements. Creating vector time with 113968 elements. Creating vector mDeltaT with 113968 elements. Creating vector time with 113968 elements. Creating vector nfix with 113968 elements. Creating vector time with 113968 elements. Creating vector efix with 113968 elements. Creating vector time with 113968 elements. Creating vector filter_north with 113968 elements. Creating vector time with 113968 elements. Creating vector filter_east with 113968 elements. Creating vector time with 113968 elements. Creating vector filter_depth with 113968 elements. Creating vector time with 113968 elements. Creating vector north_current with 113968 elements. Creating vector time with 113968 elements. Creating vector east_current with 113968 elements. Creating vector time with 113968 elements. Creating vector speed_bias with 113968 elements. Creating vector time with 113968 elements. Creating vector heading_bias with 113968 elements. Creating vector time with 113968 elements. Creating vector latitude with 113968 elements. Creating vector time with 113968 elements. Creating vector longitude with 113968 elements. Creating vector time with 113968 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/navigation.nc'); processNav(): median of positive valued depths = 23.7085 processNav(): Finding depths less than 165.9597 and times > 0 processNav(): length(Nav.depth) = 113968 processNav(): length(gindx) = 113968 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/2013/2013276/2013.276.00/gps.nc') Creating vector time with 3638 elements. Creating vector hours with 3638 elements. Creating vector time with 3638 elements. Creating vector minutes with 3638 elements. Creating vector time with 3638 elements. Creating vector seconds with 3638 elements. Creating vector time with 3638 elements. Creating vector centiSeconds with 3638 elements. Creating vector time with 3638 elements. Creating vector latitude with 3638 elements. Creating vector time with 3638 elements. Creating vector longitude with 3638 elements. Creating vector time with 3638 elements. Creating vector quality with 3638 elements. Creating vector time with 3638 elements. Creating vector numberOfSatellites with 3638 elements. Creating vector time with 3638 elements. Creating vector hdop with 3638 elements. Creating vector time with 3638 elements. Creating vector antennaHeight with 3638 elements. Creating vector time with 3638 elements. Creating vector geoHeight with 3638 elements. Creating vector time with 3638 elements. Creating vector dgpsDataAge with 3638 elements. Creating vector time with 3638 elements. Creating vector dgpsRSID with 3638 elements. Creating vector time with 3638 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/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/2013/2013276/2013.276.00/parosci.nc') Creating vector time with 224161 elements. Creating vector depth with 224161 elements. Creating vector time with 224161 elements. Creating vector temp with 224161 elements. Creating vector time with 224161 elements. Creating vector pressure with 224161 elements. Creating vector time with 224161 elements. Creating vector temp_period with 224161 elements. Creating vector time with 224161 elements. Creating vector pres_period with 224161 elements. Creating vector time with 224161 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.41449 max(Depth.data) = 51.5292 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.41449 max(Depth.data) = 51.5292 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/2013/2013276/2013.276.00/hydroscatlog.nc') Creating vector time with 91234 elements. Creating vector Seconds with 91234 elements. Creating vector time with 91234 elements. Creating vector HundrethsOfSeconds with 91234 elements. Creating vector time with 91234 elements. Creating vector Snorm1 with 91234 elements. Creating vector time with 91234 elements. Creating vector Snorm2 with 91234 elements. Creating vector time with 91234 elements. Creating vector Snorm3 with 91234 elements. Creating vector time with 91234 elements. Creating vector Gain_Status_1 with 91234 elements. Creating vector time with 91234 elements. Creating vector Gain_Status_2 with 91234 elements. Creating vector time with 91234 elements. Creating vector Gain_Status_3 with 91234 elements. Creating vector time with 91234 elements. Creating vector RawDepthValue with 91234 elements. Creating vector time with 91234 elements. Creating vector RawTempValue with 91234 elements. Creating vector time with 91234 elements. Creating vector Temperature with 91234 elements. Creating vector time with 91234 elements. Creating vector ErrorValue with 91234 elements. Creating vector time with 91234 elements. Creating vector bb470 with 91234 elements. Creating vector time with 91234 elements. Creating vector bb676 with 91234 elements. Creating vector time with 91234 elements. Creating vector fl676u with 91234 elements. Creating vector time with 91234 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/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/2013/2013276/2013.276.00/ctdDriver.nc') Creating vector time with 91212 elements. Creating vector conductivity with 91212 elements. Creating vector time with 91212 elements. Creating vector temperature with 91212 elements. Creating vector time with 91212 elements. Creating vector cond_frequency with 91212 elements. Creating vector time with 91212 elements. Creating vector temp_frequency with 91212 elements. Creating vector time with 91212 elements. Creating vector spare with 91212 elements. Creating vector time with 91212 elements. Creating vector humidity with 91212 elements. Creating vector time with 91212 elements. Creating vector flow1 with 91212 elements. Creating vector time with 91212 elements. Creating vector CDOM with 91212 elements. Creating vector time with 91212 elements. Creating vector dissolvedO2 with 91212 elements. Creating vector time with 91212 elements. Creating vector salinity with 91212 elements. Creating vector time with 91212 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/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/2013/2013276/2013.276.00/ctdDriver2.nc') Creating vector time with 91211 elements. Creating vector conductivity with 91211 elements. Creating vector time with 91211 elements. Creating vector temperature with 91211 elements. Creating vector time with 91211 elements. Creating vector cond_frequency with 91211 elements. Creating vector time with 91211 elements. Creating vector temp_frequency with 91211 elements. Creating vector time with 91211 elements. Creating vector flow2 with 91211 elements. Creating vector time with 91211 elements. Creating vector spare with 91211 elements. Creating vector time with 91211 elements. Creating vector salinity with 91211 elements. Creating vector time with 91211 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/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/2013/2013276/2013.276.00/isuslog.nc') Creating vector time with 21994 elements. Creating vector isusNitrate with 21994 elements. Creating vector time with 21994 elements. Creating vector isusTemp with 21994 elements. Creating vector time with 21994 elements. Creating vector isusQuality with 21994 elements. Creating vector time with 21994 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/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/2013/2013276/2013.276.00/biolume.nc') Creating vector time with 22446 elements. Creating vector rrr with 22446 elements. Creating vector time with 22446 elements. Creating vector cal_striing with 22446 elements. Creating vector time with 22446 elements. Creating vector avg_biolume with 22446 elements. Creating vector time with 22446 elements. Creating vector pump with 22446 elements. Creating vector time with 22446 elements. Creating vector system_voltage with 22446 elements. Creating vector time with 22446 elements. Creating vector flow with 22446 elements. Creating vector time with 22446 elements. Creating vector HV with 22446 elements. Creating vector time with 22446 elements. Creating vector reserved with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_0 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_1 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_2 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_3 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_4 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_5 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_6 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_7 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_8 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_9 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_10 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_11 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_12 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_13 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_14 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_15 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_16 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_17 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_18 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_19 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_20 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_21 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_22 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_23 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_24 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_25 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_26 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_27 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_28 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_29 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_30 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_31 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_32 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_33 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_34 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_35 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_36 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_37 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_38 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_39 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_40 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_41 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_42 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_43 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_44 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_45 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_46 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_47 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_48 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_49 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_50 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_51 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_52 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_53 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_54 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_55 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_56 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_57 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_58 with 22446 elements. Creating vector time with 22446 elements. Creating vector raw_59 with 22446 elements. Creating vector time with 22446 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/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/2013/2013276/2013.276.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (1924 x 994) with 1912456 elements. Creating vector time with 1924 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (1924 x 994) with 1912456 elements. Creating vector time with 1924 elements. Creating vector bin with 994 elements. Creating matrix countList (1924 x 994) with 1912456 elements. Creating vector time with 1924 elements. Creating vector bin with 994 elements. Creating vector LCcount with 1924 elements. Creating vector time with 1924 elements. Creating vector transCount with 1924 elements. Creating vector time with 1924 elements. Creating vector nonTransCount with 1924 elements. Creating vector time with 1924 elements. Creating vector ai_mean with 1924 elements. Creating vector time with 1924 elements. Creating vector ai_min with 1924 elements. Creating vector time with 1924 elements. Creating vector ai_max with 1924 elements. Creating vector time with 1924 elements. Creating vector ai_std with 1924 elements. Creating vector time with 1924 elements. Creating vector esd_mean with 1924 elements. Creating vector time with 1924 elements. Creating vector esd_min with 1924 elements. Creating vector time with 1924 elements. Creating vector esd_max with 1924 elements. Creating vector time with 1924 elements. Creating vector esd_std with 1924 elements. Creating vector time with 1924 elements. Creating vector countSum with 1924 elements. Creating vector time with 1924 elements. Creating vector snapshot with 1924 elements. Creating vector time with 1924 elements. Creating vector threshold with 1924 elements. Creating vector time with 1924 elements. Creating vector sampleCount with 1924 elements. Creating vector time with 1924 elements. Creating vector flowCount with 1924 elements. Creating vector time with 1924 elements. Creating vector flowTime with 1924 elements. Creating vector time with 1924 elements. Creating vector bufferStatus with 1924 elements. Creating vector time with 1924 elements. Creating vector laserLevel with 1924 elements. Creating vector time with 1924 elements. Creating vector counter with 1924 elements. Creating vector time with 1924 elements. Creating vector counterPeriod with 1924 elements. Creating vector time with 1924 elements. Creating vector laserControl with 1924 elements. Creating vector time with 1924 elements. Creating vector countUnknownFrameCharacter with 1924 elements. Creating vector time with 1924 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 1924 elements. Creating vector time with 1924 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 1924 elements. Creating vector time with 1924 elements. Creating vector flowSpeed with 1924 elements. Creating vector time with 1924 elements. Creating vector countShortLFrameError with 1924 elements. Creating vector time with 1924 elements. Creating vector countGarbledLFrame with 1924 elements. Creating vector time with 1924 elements. Creating vector cFrameEsecs with 1924 elements. Creating vector time with 1924 elements. Creating vector correctedSampleCountList with 1924 elements. Creating vector time with 1924 elements. Creating vector time with 1924 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013276/2013.276.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.276.00.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_2013.276.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 10 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_276_00_276_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_276_00_276_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_276_00_276_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 = 174 Gridding with nix = 522, iZ = 100 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 98598 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 98598 points from grid Monterey25.grd (2876 x 2447) Getting short wave radiation data from M1 for little plot above the biolume section plot Creating vector TIME with 118897 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 10/03/2013 06:30 to 10/03/2013 15:30 swr = 1.6138 69.6717 228.8185 419.1544 630.2639 763.3682 800.8821 788.9417 702.8042 535.3044 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_276_00_276_00_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/2013276_GulperTimes.txt && touch ../results/2013276_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/2013/2013276/2013.276.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013276/2013.276.00/syslog -startEsecs 1380814909.3931 -surveyName Dorado389_2013_276_00_276_00 >> ../results/2013276_GulperTimes.txt Executing: removeGulpDups.py ../results/2013276_GulperTimes.txt Bottle: 0 Time: 1380816985 Depth: 2.5214 Dist: 3.0965 Bottle: 1 Time: 1380819163 Depth: 6.3688 Dist: 6.5563 Bottle: 2 Time: 1380820764 Depth: 5.5427 Dist: 9.2674 Bottle: 3 Time: 1380822481 Depth: 12.6407 Dist: 12.0749 Bottle: 4 Time: 1380826012 Depth: 7.9127 Dist: 17.8745 Bottle: 5 Time: 1380827942 Depth: 7.3865 Dist: 21.024 Bottle: 6 Time: 1380829210 Depth: 10.4664 Dist: 23.0478 Bottle: 7 Time: 1380830594 Depth: 12.9822 Dist: 25.216 Bottle: 8 Time: 1380831946 Depth: 7.6268 Dist: 27.2926 Bottle 9 time is 323.2078 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_276_00_276_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_276_00_276_00_2column.png Elapsed time to save image: 9 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN 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_276_00_276_00_biolume.png Elapsed time to save image: 34 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_276_00_276_00_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_276_00_276_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_276_00_276_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_276_00_276_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_276_00_276_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_276_00_276_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_276_00_276_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_276_00_276_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_276_00_276_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_276_00_276_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_276_00_276_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_276_00_276_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_276_00_276_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_276_00_276_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_276_00_276_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_276_00_276_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_276_00_276_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_276_00_276_00_Optical_Backscatter_420_nm.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_276_00_276_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_276_00_276_00_Optical_Backscatter_700_nm.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_276_00_276_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_276_00_276_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_276_00_276_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_276_00_276_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_276_00_276_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_276_00_276_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_276_00_276_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_276_00_276_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_276_00_276_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in bbpRed. Interpolating anyway. 4 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 2815 NaN values in array of lon that is 20879 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 18064 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 18064 are not equal to number of Lat lon points = 20879 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_276_00_276_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_276_00_276_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_276_00_276_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_276_00_276_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 bbpRed. Interpolating anyway. 4 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_276_00_276_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_276_00_276_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_276_00_276_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_276_00_276_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_276_00_276_00 processed" mccann@mbari.org < mail_Dorado389_2013_276_00_276_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.276.00.mat Processing time: 133 seconds