Execution of AUVprocess_main version 1.86 at 2018-05-30T17:48:12Z on elvis Matlab command executed: AUVprocess_main('BIOLUME', 2007, ['346.00'], '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: 2007.346.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/ 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/2007/2007346/2007.346.00/navigation.nc') Creating vector time with 380098 elements. Creating vector mPos_x with 380098 elements. Creating vector time with 380098 elements. Creating vector mPos_y with 380098 elements. Creating vector time with 380098 elements. Creating vector mDepth with 380098 elements. Creating vector time with 380098 elements. Creating vector mGpsNorth with 380098 elements. Creating vector time with 380098 elements. Creating vector mGpsEast with 380098 elements. Creating vector time with 380098 elements. Creating vector mGpsValid with 380098 elements. Creating vector time with 380098 elements. Creating vector mPhi with 380098 elements. Creating vector time with 380098 elements. Creating vector mTheta with 380098 elements. Creating vector time with 380098 elements. Creating vector mPsi with 380098 elements. Creating vector time with 380098 elements. Creating vector mOmega_x with 380098 elements. Creating vector time with 380098 elements. Creating vector mOmega_y with 380098 elements. Creating vector time with 380098 elements. Creating vector mOmega_z with 380098 elements. Creating vector time with 380098 elements. Creating vector mPsaRange with 380098 elements. Creating vector time with 380098 elements. Creating vector mAltitude with 380098 elements. Creating vector time with 380098 elements. Creating vector mDvlAltitude with 380098 elements. Creating vector time with 380098 elements. Creating vector mWaterSpeed with 380098 elements. Creating vector time with 380098 elements. Creating vector mDvlValid with 380098 elements. Creating vector time with 380098 elements. Creating vector mDvlNewData with 380098 elements. Creating vector time with 380098 elements. Creating vector mDeltaT with 380098 elements. Creating vector time with 380098 elements. Creating vector nfix with 380098 elements. Creating vector time with 380098 elements. Creating vector efix with 380098 elements. Creating vector time with 380098 elements. Creating vector filter_north with 380098 elements. Creating vector time with 380098 elements. Creating vector filter_east with 380098 elements. Creating vector time with 380098 elements. Creating vector filter_depth with 380098 elements. Creating vector time with 380098 elements. Creating vector north_current with 380098 elements. Creating vector time with 380098 elements. Creating vector east_current with 380098 elements. Creating vector time with 380098 elements. Creating vector speed_bias with 380098 elements. Creating vector time with 380098 elements. Creating vector heading_bias with 380098 elements. Creating vector time with 380098 elements. Creating vector latitude with 380098 elements. Creating vector time with 380098 elements. Creating vector longitude with 380098 elements. Creating vector time with 380098 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/navigation.nc'); processNav(): median of positive valued depths = 16.5625 processNav(): Finding depths less than 115.9375 and times > 0 processNav(): length(Nav.depth) = 380098 processNav(): length(gindx) = 356046 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/2007/2007346/2007.346.00/gps.nc') Creating vector time with 3162 elements. Creating vector hours with 3162 elements. Creating vector time with 3162 elements. Creating vector minutes with 3162 elements. Creating vector time with 3162 elements. Creating vector seconds with 3162 elements. Creating vector time with 3162 elements. Creating vector centiSeconds with 3162 elements. Creating vector time with 3162 elements. Creating vector latitude with 3162 elements. Creating vector time with 3162 elements. Creating vector longitude with 3162 elements. Creating vector time with 3162 elements. Creating vector quality with 3162 elements. Creating vector time with 3162 elements. Creating vector numberOfSatellites with 3162 elements. Creating vector time with 3162 elements. Creating vector hdop with 3162 elements. Creating vector time with 3162 elements. Creating vector antennaHeight with 3162 elements. Creating vector time with 3162 elements. Creating vector geoHeight with 3162 elements. Creating vector time with 3162 elements. Creating vector dgpsDataAge with 3162 elements. Creating vector time with 3162 elements. Creating vector dgpsRSID with 3162 elements. Creating vector time with 3162 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/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/2007/2007346/2007.346.00/parosci.nc') Creating vector time with 667542 elements. Creating vector depth with 667542 elements. Creating vector time with 667542 elements. Creating vector temp with 667542 elements. Creating vector time with 667542 elements. Creating vector pressure with 667542 elements. Creating vector time with 667542 elements. Creating vector temp_period with 667542 elements. Creating vector time with 667542 elements. Creating vector pres_period with 667542 elements. Creating vector time with 667542 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.50738 max(Depth.data) = 251.05 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.50738 max(Depth.data) = 251.05 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/2007/2007346/2007.346.00/hydroscatlog.nc') Creating vector time with 304030 elements. Creating vector Seconds with 304030 elements. Creating vector time with 304030 elements. Creating vector HundrethsOfSeconds with 304030 elements. Creating vector time with 304030 elements. Creating vector Snorm1 with 304030 elements. Creating vector time with 304030 elements. Creating vector Snorm2 with 304030 elements. Creating vector time with 304030 elements. Creating vector Snorm3 with 304030 elements. Creating vector time with 304030 elements. Creating vector Gain_Status_1 with 304030 elements. Creating vector time with 304030 elements. Creating vector Gain_Status_2 with 304030 elements. Creating vector time with 304030 elements. Creating vector Gain_Status_3 with 304030 elements. Creating vector time with 304030 elements. Creating vector RawDepthValue with 304030 elements. Creating vector time with 304030 elements. Creating vector RawTempValue with 304030 elements. Creating vector time with 304030 elements. Creating vector Temperature with 304030 elements. Creating vector time with 304030 elements. Creating vector ErrorValue with 304030 elements. Creating vector time with 304030 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/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/2007/2007346/2007.346.00/ctdDriver.nc') Creating vector time with 304034 elements. Creating vector conductivity with 304034 elements. Creating vector time with 304034 elements. Creating vector temperature with 304034 elements. Creating vector time with 304034 elements. Creating vector cond_frequency with 304034 elements. Creating vector time with 304034 elements. Creating vector temp_frequency with 304034 elements. Creating vector time with 304034 elements. Creating vector spare with 304034 elements. Creating vector time with 304034 elements. Creating vector humidity with 304034 elements. Creating vector time with 304034 elements. Creating vector flow1 with 304034 elements. Creating vector time with 304034 elements. Creating vector CDOM with 304034 elements. Creating vector time with 304034 elements. Creating vector dissolvedO2 with 304034 elements. Creating vector time with 304034 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/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/2007/2007346/2007.346.00/ctdDriver2.nc') Creating vector time with 304049 elements. Creating vector conductivity with 304049 elements. Creating vector time with 304049 elements. Creating vector temperature with 304049 elements. Creating vector time with 304049 elements. Creating vector cond_frequency with 304049 elements. Creating vector time with 304049 elements. Creating vector temp_frequency with 304049 elements. Creating vector time with 304049 elements. Creating vector flow2 with 304049 elements. Creating vector time with 304049 elements. Creating vector spare with 304049 elements. Creating vector time with 304049 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/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/2007/2007346/2007.346.00/isuslog.nc') Creating vector time with 59073 elements. Creating vector isusNitrate with 59073 elements. Creating vector time with 59073 elements. Creating vector isusTemp with 59073 elements. Creating vector time with 59073 elements. Creating vector isusQuality with 59073 elements. Creating vector time with 59073 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/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/2007/2007346/2007.346.00/biolume.nc') Creating vector time with 76061 elements. Creating vector rrr with 76061 elements. Creating vector time with 76061 elements. Creating vector cal_striing with 76061 elements. Creating vector time with 76061 elements. Creating vector pump with 76061 elements. Creating vector time with 76061 elements. Creating vector flow with 76061 elements. Creating vector time with 76061 elements. Creating vector humidity with 76061 elements. Creating vector time with 76061 elements. Creating vector temperature with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_0 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_1 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_2 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_3 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_4 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_5 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_6 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_7 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_8 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_9 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_10 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_11 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_12 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_13 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_14 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_15 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_16 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_17 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_18 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_19 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_20 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_21 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_22 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_23 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_24 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_25 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_26 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_27 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_28 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_29 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_30 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_31 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_32 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_33 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_34 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_35 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_36 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_37 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_38 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_39 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_40 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_41 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_42 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_43 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_44 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_45 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_46 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_47 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_48 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_49 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_50 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_51 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_52 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_53 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_54 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_55 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_56 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_57 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_58 with 76061 elements. Creating vector time with 76061 elements. Creating vector raw_59 with 76061 elements. Creating vector time with 76061 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/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/2007/2007346/2007.346.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (4841 x 994) with 4811954 elements. Creating vector time with 4841 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (4841 x 994) with 4811954 elements. Creating vector time with 4841 elements. Creating vector bin with 994 elements. Creating matrix countList (4841 x 994) with 4811954 elements. Creating vector time with 4841 elements. Creating vector bin with 994 elements. Creating vector LCcount with 4841 elements. Creating vector time with 4841 elements. Creating vector transCount with 4841 elements. Creating vector time with 4841 elements. Creating vector nonTransCount with 4841 elements. Creating vector time with 4841 elements. Creating vector ai_mean with 4841 elements. Creating vector time with 4841 elements. Creating vector ai_min with 4841 elements. Creating vector time with 4841 elements. Creating vector ai_max with 4841 elements. Creating vector time with 4841 elements. Creating vector ai_std with 4841 elements. Creating vector time with 4841 elements. Creating vector esd_mean with 4841 elements. Creating vector time with 4841 elements. Creating vector esd_min with 4841 elements. Creating vector time with 4841 elements. Creating vector esd_max with 4841 elements. Creating vector time with 4841 elements. Creating vector esd_std with 4841 elements. Creating vector time with 4841 elements. Creating vector countSum with 4841 elements. Creating vector time with 4841 elements. Creating vector snapshot with 4841 elements. Creating vector time with 4841 elements. Creating vector threshold with 4841 elements. Creating vector time with 4841 elements. Creating vector sampleCount with 4841 elements. Creating vector time with 4841 elements. Creating vector flowCount with 4841 elements. Creating vector time with 4841 elements. Creating vector flowTime with 4841 elements. Creating vector time with 4841 elements. Creating vector bufferStatus with 4841 elements. Creating vector time with 4841 elements. Creating vector laserLevel with 4841 elements. Creating vector time with 4841 elements. Creating vector counter with 4841 elements. Creating vector time with 4841 elements. Creating vector counterPeriod with 4841 elements. Creating vector time with 4841 elements. Creating vector laserControl with 4841 elements. Creating vector time with 4841 elements. Creating vector countUnknownFrameCharacter with 4841 elements. Creating vector time with 4841 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 4841 elements. Creating vector time with 4841 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 4841 elements. Creating vector time with 4841 elements. Creating vector flowSpeed with 4841 elements. Creating vector time with 4841 elements. Creating vector countShortLFrameError with 4841 elements. Creating vector time with 4841 elements. Creating vector countGarbledLFrame with 4841 elements. Creating vector time with 4841 elements. Creating vector correctedSampleCountList with 4841 elements. Creating vector time with 4841 elements. Creating vector time with 4841 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007346/2007.346.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007.346.00.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_2007.346.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 34 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_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 = 828 Gridding with nix = 2484, iZ = 228 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... bbp470 bbp676 fl676_uncorr N BL BLflow LOPC count [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 355) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] transCount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 357) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] nonTransCount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 359) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] LCcount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 361) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB470 cvarname = gB676 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount cvarname = gLOPCtransCount cvarname = gLOPCnonTransCount cvarname = gLOPCLCcount Encountered 0 NaN values in array of lon that is 355898 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 355898 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 119039 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 12/11/2007 14:30 to 12/12/2007 13:30 swr = 275.2727 111.4800 21.8000 3.1200 3.3000 2.8400 3.7600 3.8000 3.5800 3.8600 3.7400 3.7400 3.7200 3.8200 4.0600 3.8600 4.2840 17.4614 137.4000 259.6616 318.5780 395.9418 483.2959 435.7389 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2007346_GulperTimes.txt && touch ../results/2007346_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/2007/2007346/2007.346.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2007/2007346/2007.346.00/syslog -startEsecs 1197417948.0428 -surveyName Dorado389_2007_346_00_346_00 >> ../results/2007346_GulperTimes.txt Executing: removeGulpDups.py ../results/2007346_GulperTimes.txt Bottle: 0 Time: 1197451561.4401 Depth: 80.1021 Dist: 39.7616 Bottle 1 time is 17.0288 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Bottle: 2 Time: 1197457255.64 Depth: 20.6526 Dist: 45.8533 Bottle: 3 Time: 1197457501.4432 Depth: 80.6288 Dist: 46.127 Bottle 4 time is 19.8286 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Bottle 5 time is 339.4267 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Bottle: 6 Time: 1197462384.6387 Depth: 104.6506 Dist: 51.3485 Bottle: 7 Time: 1197462467.043 Depth: 79.3706 Dist: 51.426 Bottle: 8 Time: 1197462644.4409 Depth: 19.0443 Dist: 51.6121 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_gridded.mat outvarstr = 'gF gT gN gS gD gO gB470 gB676 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 gB470 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB676 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_2007_346_00_346_00_2column.png Elapsed time to save image: 21 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 gB470 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB676 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_2007_346_00_346_00_biolume.png Elapsed time to save image: 66 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 gB470 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB676 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_2007_346_00_346_00_lopc.png Elapsed time to save image: 16 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_2007_346_00_346_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_2column.png... Copied to /mbari/AUVCTD/surveys/2007/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2007/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2007/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2007/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2007/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2007/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_2007_346_00_346_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2007/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_2007_346_00_346_00_Salinity.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2007/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_2007_346_00_346_00_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2007/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_2007_346_00_346_00_Oxygen.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2007/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @470 nm', jetplus, varlimits(5,:), hs2.bbp470, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_00_Optical_Backscatter_470_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_00_Optical_Backscatter_470_nm.kmz... Copied to /mbari/AUVCTD/surveys/2007/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_00_Optical_Backscatter_676_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_00_Optical_Backscatter_676_nm.kmz... Copied to /mbari/AUVCTD/surveys/2007/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.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2007/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_2007_346_00_346_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2007/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 do interp1: The grid vectors must contain unique points. Did not write KML for this variable. Rethrowing error. Could not create .kmz for LOPC Total Count Creating Dorado389_2007_346_00_346_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00.kml... Copied to /mbari/AUVCTD/surveys/2007/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_346_00_346_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_2007_346_00_346_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 266 NaNs found in bbpBlue. Interpolating anyway. 256 NaNs found in bbpRed. Interpolating anyway. 16 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 24 NaN values in array of lon that is 59073 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 59049 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 59049 are not equal to number of Lat lon points = 59073 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_2007_346_00_346_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00.txt... Copied to /mbari/AUVCTD/surveys/2007/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2007/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... 266 NaNs found in bbpBlue. Interpolating anyway. 256 NaNs found in bbpRed. Interpolating anyway. 16 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_2007_346_00_346_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2007/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_2007_346_00_346_00.nc... Copied to /mbari/AUVCTD/surveys/2007/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2007/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_346_00_346_00.mat... Copied to /mbari/AUVCTD/surveys/2007/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2007_346_00_346_00 processed" mccann@mbari.org < mail_Dorado389_2007_346_00_346_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007.346.00.mat Processing time: 454 seconds