Execution of AUVprocess_main version 1.86 at 2018-05-24T21:04:14Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2013, ['301.03'], '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: 2013.301.03 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/ 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/2013/2013301/2013.301.03/navigation.nc') Creating vector time with 932 elements. Creating vector mPos_x with 932 elements. Creating vector time with 932 elements. Creating vector mPos_y with 932 elements. Creating vector time with 932 elements. Creating vector mDepth with 932 elements. Creating vector time with 932 elements. Creating vector mGpsNorth with 932 elements. Creating vector time with 932 elements. Creating vector mGpsEast with 932 elements. Creating vector time with 932 elements. Creating vector mGpsValid with 932 elements. Creating vector time with 932 elements. Creating vector mPhi with 932 elements. Creating vector time with 932 elements. Creating vector mTheta with 932 elements. Creating vector time with 932 elements. Creating vector mPsi with 932 elements. Creating vector time with 932 elements. Creating vector mOmega_x with 932 elements. Creating vector time with 932 elements. Creating vector mOmega_y with 932 elements. Creating vector time with 932 elements. Creating vector mOmega_z with 932 elements. Creating vector time with 932 elements. Creating vector mPsaRange with 932 elements. Creating vector time with 932 elements. Creating vector mAltitude with 932 elements. Creating vector time with 932 elements. Creating vector mDvlAltitude with 932 elements. Creating vector time with 932 elements. Creating vector mEchoAltitude with 932 elements. Creating vector time with 932 elements. Creating vector mEchoHorizRange with 932 elements. Creating vector time with 932 elements. Creating vector mEchoAltitudeLast with 932 elements. Creating vector time with 932 elements. Creating vector mEchoHorizRangeLast with 932 elements. Creating vector time with 932 elements. Creating vector mEchoNumOfPings with 932 elements. Creating vector time with 932 elements. Creating vector mWaterSpeed with 932 elements. Creating vector time with 932 elements. Creating vector mDvlValid with 932 elements. Creating vector time with 932 elements. Creating vector mDvlNewData with 932 elements. Creating vector time with 932 elements. Creating vector mDeltaT with 932 elements. Creating vector time with 932 elements. Creating vector nfix with 932 elements. Creating vector time with 932 elements. Creating vector efix with 932 elements. Creating vector time with 932 elements. Creating vector filter_north with 932 elements. Creating vector time with 932 elements. Creating vector filter_east with 932 elements. Creating vector time with 932 elements. Creating vector filter_depth with 932 elements. Creating vector time with 932 elements. Creating vector north_current with 932 elements. Creating vector time with 932 elements. Creating vector east_current with 932 elements. Creating vector time with 932 elements. Creating vector speed_bias with 932 elements. Creating vector time with 932 elements. Creating vector heading_bias with 932 elements. Creating vector time with 932 elements. Creating vector latitude with 932 elements. Creating vector time with 932 elements. Creating vector longitude with 932 elements. Creating vector time with 932 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/navigation.nc'); processNav(): median of positive valued depths = 4.7602 processNav(): Finding depths less than 33.3216 and times > 0 processNav(): length(Nav.depth) = 932 processNav(): length(gindx) = 932 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/2013/2013301/2013.301.03/gps.nc') Creating vector time with 122 elements. Creating vector hours with 122 elements. Creating vector time with 122 elements. Creating vector minutes with 122 elements. Creating vector time with 122 elements. Creating vector seconds with 122 elements. Creating vector time with 122 elements. Creating vector centiSeconds with 122 elements. Creating vector time with 122 elements. Creating vector latitude with 122 elements. Creating vector time with 122 elements. Creating vector longitude with 122 elements. Creating vector time with 122 elements. Creating vector quality with 122 elements. Creating vector time with 122 elements. Creating vector numberOfSatellites with 122 elements. Creating vector time with 122 elements. Creating vector hdop with 122 elements. Creating vector time with 122 elements. Creating vector antennaHeight with 122 elements. Creating vector time with 122 elements. Creating vector geoHeight with 122 elements. Creating vector time with 122 elements. Creating vector dgpsDataAge with 122 elements. Creating vector time with 122 elements. Creating vector dgpsRSID with 122 elements. Creating vector time with 122 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/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/2013/2013301/2013.301.03/parosci.nc') Creating vector time with 2199 elements. Creating vector depth with 2199 elements. Creating vector time with 2199 elements. Creating vector temp with 2199 elements. Creating vector time with 2199 elements. Creating vector pressure with 2199 elements. Creating vector time with 2199 elements. Creating vector temp_period with 2199 elements. Creating vector time with 2199 elements. Creating vector pres_period with 2199 elements. Creating vector time with 2199 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.21877 max(Depth.data) = 7.882 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.21877 max(Depth.data) = 7.882 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/2013/2013301/2013.301.03/hydroscatlog.nc') Creating vector time with 877 elements. Creating vector Seconds with 877 elements. Creating vector time with 877 elements. Creating vector HundrethsOfSeconds with 877 elements. Creating vector time with 877 elements. Creating vector Snorm1 with 877 elements. Creating vector time with 877 elements. Creating vector Snorm2 with 877 elements. Creating vector time with 877 elements. Creating vector Snorm3 with 877 elements. Creating vector time with 877 elements. Creating vector Gain_Status_1 with 877 elements. Creating vector time with 877 elements. Creating vector Gain_Status_2 with 877 elements. Creating vector time with 877 elements. Creating vector Gain_Status_3 with 877 elements. Creating vector time with 877 elements. Creating vector RawDepthValue with 877 elements. Creating vector time with 877 elements. Creating vector RawTempValue with 877 elements. Creating vector time with 877 elements. Creating vector Temperature with 877 elements. Creating vector time with 877 elements. Creating vector ErrorValue with 877 elements. Creating vector time with 877 elements. Creating vector bb470 with 877 elements. Creating vector time with 877 elements. Creating vector bb676 with 877 elements. Creating vector time with 877 elements. Creating vector fl676u with 877 elements. Creating vector time with 877 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/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/2013/2013301/2013.301.03/ctdDriver.nc') Creating vector time with 786 elements. Creating vector conductivity with 786 elements. Creating vector time with 786 elements. Creating vector temperature with 786 elements. Creating vector time with 786 elements. Creating vector cond_frequency with 786 elements. Creating vector time with 786 elements. Creating vector temp_frequency with 786 elements. Creating vector time with 786 elements. Creating vector spare with 786 elements. Creating vector time with 786 elements. Creating vector humidity with 786 elements. Creating vector time with 786 elements. Creating vector flow1 with 786 elements. Creating vector time with 786 elements. Creating vector CDOM with 786 elements. Creating vector time with 786 elements. Creating vector dissolvedO2 with 786 elements. Creating vector time with 786 elements. Creating vector salinity with 786 elements. Creating vector time with 786 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/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/2013/2013301/2013.301.03/ctdDriver2.nc') Creating vector time with 788 elements. Creating vector conductivity with 788 elements. Creating vector time with 788 elements. Creating vector temperature with 788 elements. Creating vector time with 788 elements. Creating vector cond_frequency with 788 elements. Creating vector time with 788 elements. Creating vector temp_frequency with 788 elements. Creating vector time with 788 elements. Creating vector flow2 with 788 elements. Creating vector time with 788 elements. Creating vector spare with 788 elements. Creating vector time with 788 elements. Creating vector salinity with 788 elements. Creating vector time with 788 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/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/2013/2013301/2013.301.03/isuslog.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/isuslog.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/isuslog.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/isuslog.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting ISUS structure to NaN values. Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/biolume.nc') Creating vector time with 221 elements. Creating vector rrr with 221 elements. Creating vector time with 221 elements. Creating vector cal_striing with 221 elements. Creating vector time with 221 elements. Creating vector avg_biolume with 221 elements. Creating vector time with 221 elements. Creating vector pump with 221 elements. Creating vector time with 221 elements. Creating vector system_voltage with 221 elements. Creating vector time with 221 elements. Creating vector flow with 221 elements. Creating vector time with 221 elements. Creating vector HV with 221 elements. Creating vector time with 221 elements. Creating vector reserved with 221 elements. Creating vector time with 221 elements. Creating vector raw_0 with 221 elements. Creating vector time with 221 elements. Creating vector raw_1 with 221 elements. Creating vector time with 221 elements. Creating vector raw_2 with 221 elements. Creating vector time with 221 elements. Creating vector raw_3 with 221 elements. Creating vector time with 221 elements. Creating vector raw_4 with 221 elements. Creating vector time with 221 elements. Creating vector raw_5 with 221 elements. Creating vector time with 221 elements. Creating vector raw_6 with 221 elements. Creating vector time with 221 elements. Creating vector raw_7 with 221 elements. Creating vector time with 221 elements. Creating vector raw_8 with 221 elements. Creating vector time with 221 elements. Creating vector raw_9 with 221 elements. Creating vector time with 221 elements. Creating vector raw_10 with 221 elements. Creating vector time with 221 elements. Creating vector raw_11 with 221 elements. Creating vector time with 221 elements. Creating vector raw_12 with 221 elements. Creating vector time with 221 elements. Creating vector raw_13 with 221 elements. Creating vector time with 221 elements. Creating vector raw_14 with 221 elements. Creating vector time with 221 elements. Creating vector raw_15 with 221 elements. Creating vector time with 221 elements. Creating vector raw_16 with 221 elements. Creating vector time with 221 elements. Creating vector raw_17 with 221 elements. Creating vector time with 221 elements. Creating vector raw_18 with 221 elements. Creating vector time with 221 elements. Creating vector raw_19 with 221 elements. Creating vector time with 221 elements. Creating vector raw_20 with 221 elements. Creating vector time with 221 elements. Creating vector raw_21 with 221 elements. Creating vector time with 221 elements. Creating vector raw_22 with 221 elements. Creating vector time with 221 elements. Creating vector raw_23 with 221 elements. Creating vector time with 221 elements. Creating vector raw_24 with 221 elements. Creating vector time with 221 elements. Creating vector raw_25 with 221 elements. Creating vector time with 221 elements. Creating vector raw_26 with 221 elements. Creating vector time with 221 elements. Creating vector raw_27 with 221 elements. Creating vector time with 221 elements. Creating vector raw_28 with 221 elements. Creating vector time with 221 elements. Creating vector raw_29 with 221 elements. Creating vector time with 221 elements. Creating vector raw_30 with 221 elements. Creating vector time with 221 elements. Creating vector raw_31 with 221 elements. Creating vector time with 221 elements. Creating vector raw_32 with 221 elements. Creating vector time with 221 elements. Creating vector raw_33 with 221 elements. Creating vector time with 221 elements. Creating vector raw_34 with 221 elements. Creating vector time with 221 elements. Creating vector raw_35 with 221 elements. Creating vector time with 221 elements. Creating vector raw_36 with 221 elements. Creating vector time with 221 elements. Creating vector raw_37 with 221 elements. Creating vector time with 221 elements. Creating vector raw_38 with 221 elements. Creating vector time with 221 elements. Creating vector raw_39 with 221 elements. Creating vector time with 221 elements. Creating vector raw_40 with 221 elements. Creating vector time with 221 elements. Creating vector raw_41 with 221 elements. Creating vector time with 221 elements. Creating vector raw_42 with 221 elements. Creating vector time with 221 elements. Creating vector raw_43 with 221 elements. Creating vector time with 221 elements. Creating vector raw_44 with 221 elements. Creating vector time with 221 elements. Creating vector raw_45 with 221 elements. Creating vector time with 221 elements. Creating vector raw_46 with 221 elements. Creating vector time with 221 elements. Creating vector raw_47 with 221 elements. Creating vector time with 221 elements. Creating vector raw_48 with 221 elements. Creating vector time with 221 elements. Creating vector raw_49 with 221 elements. Creating vector time with 221 elements. Creating vector raw_50 with 221 elements. Creating vector time with 221 elements. Creating vector raw_51 with 221 elements. Creating vector time with 221 elements. Creating vector raw_52 with 221 elements. Creating vector time with 221 elements. Creating vector raw_53 with 221 elements. Creating vector time with 221 elements. Creating vector raw_54 with 221 elements. Creating vector time with 221 elements. Creating vector raw_55 with 221 elements. Creating vector time with 221 elements. Creating vector raw_56 with 221 elements. Creating vector time with 221 elements. Creating vector raw_57 with 221 elements. Creating vector time with 221 elements. Creating vector raw_58 with 221 elements. Creating vector time with 221 elements. Creating vector raw_59 with 221 elements. Creating vector time with 221 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/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/2013/2013301/2013.301.03/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (21 x 994) with 20874 elements. Creating vector time with 21 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (21 x 994) with 20874 elements. Creating vector time with 21 elements. Creating vector bin with 994 elements. Creating matrix countList (21 x 994) with 20874 elements. Creating vector time with 21 elements. Creating vector bin with 994 elements. Creating vector LCcount with 21 elements. Creating vector time with 21 elements. Creating vector transCount with 21 elements. Creating vector time with 21 elements. Creating vector nonTransCount with 21 elements. Creating vector time with 21 elements. Creating vector ai_mean with 21 elements. Creating vector time with 21 elements. Creating vector ai_min with 21 elements. Creating vector time with 21 elements. Creating vector ai_max with 21 elements. Creating vector time with 21 elements. Creating vector ai_std with 21 elements. Creating vector time with 21 elements. Creating vector esd_mean with 21 elements. Creating vector time with 21 elements. Creating vector esd_min with 21 elements. Creating vector time with 21 elements. Creating vector esd_max with 21 elements. Creating vector time with 21 elements. Creating vector esd_std with 21 elements. Creating vector time with 21 elements. Creating vector countSum with 21 elements. Creating vector time with 21 elements. Creating vector snapshot with 21 elements. Creating vector time with 21 elements. Creating vector threshold with 21 elements. Creating vector time with 21 elements. Creating vector sampleCount with 21 elements. Creating vector time with 21 elements. Creating vector flowCount with 21 elements. Creating vector time with 21 elements. Creating vector flowTime with 21 elements. Creating vector time with 21 elements. Creating vector bufferStatus with 21 elements. Creating vector time with 21 elements. Creating vector laserLevel with 21 elements. Creating vector time with 21 elements. Creating vector counter with 21 elements. Creating vector time with 21 elements. Creating vector counterPeriod with 21 elements. Creating vector time with 21 elements. Creating vector laserControl with 21 elements. Creating vector time with 21 elements. Creating vector countUnknownFrameCharacter with 21 elements. Creating vector time with 21 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 21 elements. Creating vector time with 21 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 21 elements. Creating vector time with 21 elements. Creating vector flowSpeed with 21 elements. Creating vector time with 21 elements. Creating vector countShortLFrameError with 21 elements. Creating vector time with 21 elements. Creating vector countGarbledLFrame with 21 elements. Creating vector time with 21 elements. Creating vector cFrameEsecs with 21 elements. Creating vector time with 21 elements. Creating vector correctedSampleCountList with 21 elements. Creating vector time with 21 elements. Creating vector time with 21 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.03/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.301.03.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_2013.301.03.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... matchDVLtoGPS(): No underwater portion identified with tDiffCrit = 720 matchDVLtoGPS(): finding gap with almostMaxDiff = 104.0028 Looping over 1 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03.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 = 4 Gridding with nix = 12, iZ = 13 Using mean boxcar filter of vector... Using mean boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Gridding... T S O Using median boxcar filter of vector... Using median boxcar filter of vector... Using median boxcar filter of vector... bbp420 bbp700 fl700_uncorr N Only one good point - NaNing the gN array. BL BLflow LOPC 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 No valid data for 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 747 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 747 points from grid Monterey25.grd (2876 x 2447) Getting short wave radiation data from M1 for little plot above the biolume section plot Creating vector TIME with 118898 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 10/28/2013 08:30 to 10/28/2013 10:29 swr = 47.1321 112.5679 262.2445 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03_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/2013301_GulperTimes.txt && touch ../results/2013301_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/2013/2013301/2013.301.03/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013301/2013.301.03/syslog -startEsecs 1382981015.1044 -surveyName Dorado389_2013_301_03_301_03 >> ../results/2013301_GulperTimes.txt Executing: removeGulpDups.py ../results/2013301_GulperTimes.txt Bottle: 6 Time: 1382981119 Depth: 3.9247 Dist: 0.057669 Bottle: 3 Time: 1382981119 Depth: 3.9247 Dist: 0.057669 Bottle: 7 Time: 1382981119 Depth: 3.9247 Dist: 0.057669 Bottle: 9 Time: 1382981119 Depth: 3.9247 Dist: 0.057669 Bottle: 2 Time: 1382981119 Depth: 3.9247 Dist: 0.057669 Bottle: 8 Time: 1382981119 Depth: 3.9247 Dist: 0.057669 Bottle: 1 Time: 1382981119 Depth: 3.9247 Dist: 0.057669 Bottle: 4 Time: 1382981119 Depth: 3.9247 Dist: 0.057669 Bottle: 0 Time: 1382981119 Depth: 3.9247 Dist: 0.057669 Bottle: 5 Time: 1382981119 Depth: 3.9247 Dist: 0.057669 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03_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 2Column contouring gridded variable gT 2Column contouring gridded variable gS 2Column contouring gridded variable gN 2Column contouring gridded variable gO 2Column contouring gridded variable gB420 2Column contouring gridded variable gB700 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03_2column.png Elapsed time to save image: 4 seconds Biolume contouring gridded variable gD Biolume contouring gridded variable gT Biolume contouring gridded variable gS Biolume contouring gridded variable gN Biolume contouring gridded variable gO Biolume contouring gridded variable gB420 Biolume contouring gridded variable gB700 Biolume contouring gridded variable gF Biolume contouring gridded variable gBL Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03_biolume.png Elapsed time to save image: 19 seconds 2Column contouring gridded variable gLOPCcount 2Column contouring gridded variable gLOPCtransCount 2Column contouring gridded variable gLOPCnonTransCount 2Column contouring gridded variable gLOPCLCcount 2Column contouring gridded variable gT 2Column contouring gridded variable gB420 2Column contouring gridded variable gB700 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03_lopc.png Elapsed time to save image: 4 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_301_03_301_03_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03_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_301_03_301_03_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_301_03_301_03_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_301_03_301_03_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_301_03_301_03_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_301_03_301_03_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_301_03_301_03_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_03_301_03_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_301_03_301_03_Salinity.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_03_301_03_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath); length(v_esecs(gindx)) = which is less than 2. Not processing. updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_03_301_03_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_03_301_03_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_301_03_301_03_Oxygen.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_03_301_03_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_301_03_301_03_Optical_Backscatter_420_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_03_301_03_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_301_03_301_03_Optical_Backscatter_700_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_03_301_03_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_301_03_301_03_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_03_301_03_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_301_03_301_03_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_03_301_03_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_301_03_301_03.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03.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_301_03_301_03_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_301_03_301_03.mat ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Encountered 5 NaN values in array of lon that is 79 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 74 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 74 are not equal to number of Lat lon points = 79 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_301_03_301_03.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03.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_301_03_301_03_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2013/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_03_301_03_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_301_03_301_03.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_301_03_301_03_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_301_03_301_03.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_301_03_301_03 processed" mccann@mbari.org < mail_Dorado389_2013_301_03_301_03.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.301.03.mat Processing time: 19 seconds