Execution of AUVprocess_main version 1.86 at 2018-05-24T21:05:17Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2013, ['301.04'], '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: 2013.301.04 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/ 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/2013/2013301/2013.301.04/navigation.nc') Creating vector time with 32854 elements. Creating vector mPos_x with 32854 elements. Creating vector time with 32854 elements. Creating vector mPos_y with 32854 elements. Creating vector time with 32854 elements. Creating vector mDepth with 32854 elements. Creating vector time with 32854 elements. Creating vector mGpsNorth with 32854 elements. Creating vector time with 32854 elements. Creating vector mGpsEast with 32854 elements. Creating vector time with 32854 elements. Creating vector mGpsValid with 32854 elements. Creating vector time with 32854 elements. Creating vector mPhi with 32854 elements. Creating vector time with 32854 elements. Creating vector mTheta with 32854 elements. Creating vector time with 32854 elements. Creating vector mPsi with 32854 elements. Creating vector time with 32854 elements. Creating vector mOmega_x with 32854 elements. Creating vector time with 32854 elements. Creating vector mOmega_y with 32854 elements. Creating vector time with 32854 elements. Creating vector mOmega_z with 32854 elements. Creating vector time with 32854 elements. Creating vector mPsaRange with 32854 elements. Creating vector time with 32854 elements. Creating vector mAltitude with 32854 elements. Creating vector time with 32854 elements. Creating vector mDvlAltitude with 32854 elements. Creating vector time with 32854 elements. Creating vector mEchoAltitude with 32854 elements. Creating vector time with 32854 elements. Creating vector mEchoHorizRange with 32854 elements. Creating vector time with 32854 elements. Creating vector mEchoAltitudeLast with 32854 elements. Creating vector time with 32854 elements. Creating vector mEchoHorizRangeLast with 32854 elements. Creating vector time with 32854 elements. Creating vector mEchoNumOfPings with 32854 elements. Creating vector time with 32854 elements. Creating vector mWaterSpeed with 32854 elements. Creating vector time with 32854 elements. Creating vector mDvlValid with 32854 elements. Creating vector time with 32854 elements. Creating vector mDvlNewData with 32854 elements. Creating vector time with 32854 elements. Creating vector mDeltaT with 32854 elements. Creating vector time with 32854 elements. Creating vector nfix with 32854 elements. Creating vector time with 32854 elements. Creating vector efix with 32854 elements. Creating vector time with 32854 elements. Creating vector filter_north with 32854 elements. Creating vector time with 32854 elements. Creating vector filter_east with 32854 elements. Creating vector time with 32854 elements. Creating vector filter_depth with 32854 elements. Creating vector time with 32854 elements. Creating vector north_current with 32854 elements. Creating vector time with 32854 elements. Creating vector east_current with 32854 elements. Creating vector time with 32854 elements. Creating vector speed_bias with 32854 elements. Creating vector time with 32854 elements. Creating vector heading_bias with 32854 elements. Creating vector time with 32854 elements. Creating vector latitude with 32854 elements. Creating vector time with 32854 elements. Creating vector longitude with 32854 elements. Creating vector time with 32854 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/navigation.nc'); processNav(): median of positive valued depths = 10.9659 processNav(): Finding depths less than 76.7616 and times > 0 processNav(): length(Nav.depth) = 32854 processNav(): length(gindx) = 32854 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/2013/2013301/2013.301.04/gps.nc') Creating vector time with 625 elements. Creating vector hours with 625 elements. Creating vector time with 625 elements. Creating vector minutes with 625 elements. Creating vector time with 625 elements. Creating vector seconds with 625 elements. Creating vector time with 625 elements. Creating vector centiSeconds with 625 elements. Creating vector time with 625 elements. Creating vector latitude with 625 elements. Creating vector time with 625 elements. Creating vector longitude with 625 elements. Creating vector time with 625 elements. Creating vector quality with 625 elements. Creating vector time with 625 elements. Creating vector numberOfSatellites with 625 elements. Creating vector time with 625 elements. Creating vector hdop with 625 elements. Creating vector time with 625 elements. Creating vector antennaHeight with 625 elements. Creating vector time with 625 elements. Creating vector geoHeight with 625 elements. Creating vector time with 625 elements. Creating vector dgpsDataAge with 625 elements. Creating vector time with 625 elements. Creating vector dgpsRSID with 625 elements. Creating vector time with 625 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/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/2013/2013301/2013.301.04/parosci.nc') Creating vector time with 65011 elements. Creating vector depth with 65011 elements. Creating vector time with 65011 elements. Creating vector temp with 65011 elements. Creating vector time with 65011 elements. Creating vector pressure with 65011 elements. Creating vector time with 65011 elements. Creating vector temp_period with 65011 elements. Creating vector time with 65011 elements. Creating vector pres_period with 65011 elements. Creating vector time with 65011 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.31927 max(Depth.data) = 30.4105 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.31927 max(Depth.data) = 30.4105 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/2013/2013301/2013.301.04/hydroscatlog.nc') Creating vector time with 26402 elements. Creating vector Seconds with 26402 elements. Creating vector time with 26402 elements. Creating vector HundrethsOfSeconds with 26402 elements. Creating vector time with 26402 elements. Creating vector Snorm1 with 26402 elements. Creating vector time with 26402 elements. Creating vector Snorm2 with 26402 elements. Creating vector time with 26402 elements. Creating vector Snorm3 with 26402 elements. Creating vector time with 26402 elements. Creating vector Gain_Status_1 with 26402 elements. Creating vector time with 26402 elements. Creating vector Gain_Status_2 with 26402 elements. Creating vector time with 26402 elements. Creating vector Gain_Status_3 with 26402 elements. Creating vector time with 26402 elements. Creating vector RawDepthValue with 26402 elements. Creating vector time with 26402 elements. Creating vector RawTempValue with 26402 elements. Creating vector time with 26402 elements. Creating vector Temperature with 26402 elements. Creating vector time with 26402 elements. Creating vector ErrorValue with 26402 elements. Creating vector time with 26402 elements. Creating vector bb470 with 26402 elements. Creating vector time with 26402 elements. Creating vector bb676 with 26402 elements. Creating vector time with 26402 elements. Creating vector fl676u with 26402 elements. Creating vector time with 26402 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/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/2013/2013301/2013.301.04/ctdDriver.nc') Creating vector time with 26328 elements. Creating vector conductivity with 26328 elements. Creating vector time with 26328 elements. Creating vector temperature with 26328 elements. Creating vector time with 26328 elements. Creating vector cond_frequency with 26328 elements. Creating vector time with 26328 elements. Creating vector temp_frequency with 26328 elements. Creating vector time with 26328 elements. Creating vector spare with 26328 elements. Creating vector time with 26328 elements. Creating vector humidity with 26328 elements. Creating vector time with 26328 elements. Creating vector flow1 with 26328 elements. Creating vector time with 26328 elements. Creating vector CDOM with 26328 elements. Creating vector time with 26328 elements. Creating vector dissolvedO2 with 26328 elements. Creating vector time with 26328 elements. Creating vector salinity with 26328 elements. Creating vector time with 26328 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/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/2013/2013301/2013.301.04/ctdDriver2.nc') Creating vector time with 26326 elements. Creating vector conductivity with 26326 elements. Creating vector time with 26326 elements. Creating vector temperature with 26326 elements. Creating vector time with 26326 elements. Creating vector cond_frequency with 26326 elements. Creating vector time with 26326 elements. Creating vector temp_frequency with 26326 elements. Creating vector time with 26326 elements. Creating vector flow2 with 26326 elements. Creating vector time with 26326 elements. Creating vector spare with 26326 elements. Creating vector time with 26326 elements. Creating vector salinity with 26326 elements. Creating vector time with 26326 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/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/2013/2013301/2013.301.04/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/2013/2013301/2013.301.04/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/2013/2013301/2013.301.04/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/2013/2013301/2013.301.04/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/2013/2013301/2013.301.04/biolume.nc') Creating vector time with 6499 elements. Creating vector rrr with 6499 elements. Creating vector time with 6499 elements. Creating vector cal_striing with 6499 elements. Creating vector time with 6499 elements. Creating vector avg_biolume with 6499 elements. Creating vector time with 6499 elements. Creating vector pump with 6499 elements. Creating vector time with 6499 elements. Creating vector system_voltage with 6499 elements. Creating vector time with 6499 elements. Creating vector flow with 6499 elements. Creating vector time with 6499 elements. Creating vector HV with 6499 elements. Creating vector time with 6499 elements. Creating vector reserved with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_0 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_1 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_2 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_3 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_4 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_5 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_6 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_7 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_8 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_9 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_10 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_11 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_12 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_13 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_14 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_15 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_16 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_17 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_18 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_19 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_20 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_21 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_22 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_23 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_24 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_25 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_26 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_27 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_28 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_29 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_30 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_31 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_32 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_33 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_34 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_35 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_36 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_37 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_38 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_39 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_40 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_41 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_42 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_43 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_44 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_45 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_46 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_47 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_48 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_49 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_50 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_51 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_52 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_53 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_54 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_55 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_56 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_57 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_58 with 6499 elements. Creating vector time with 6499 elements. Creating vector raw_59 with 6499 elements. Creating vector time with 6499 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/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/2013/2013301/2013.301.04/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (628 x 994) with 624232 elements. Creating vector time with 628 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (628 x 994) with 624232 elements. Creating vector time with 628 elements. Creating vector bin with 994 elements. Creating matrix countList (628 x 994) with 624232 elements. Creating vector time with 628 elements. Creating vector bin with 994 elements. Creating vector LCcount with 628 elements. Creating vector time with 628 elements. Creating vector transCount with 628 elements. Creating vector time with 628 elements. Creating vector nonTransCount with 628 elements. Creating vector time with 628 elements. Creating vector ai_mean with 628 elements. Creating vector time with 628 elements. Creating vector ai_min with 628 elements. Creating vector time with 628 elements. Creating vector ai_max with 628 elements. Creating vector time with 628 elements. Creating vector ai_std with 628 elements. Creating vector time with 628 elements. Creating vector esd_mean with 628 elements. Creating vector time with 628 elements. Creating vector esd_min with 628 elements. Creating vector time with 628 elements. Creating vector esd_max with 628 elements. Creating vector time with 628 elements. Creating vector esd_std with 628 elements. Creating vector time with 628 elements. Creating vector countSum with 628 elements. Creating vector time with 628 elements. Creating vector snapshot with 628 elements. Creating vector time with 628 elements. Creating vector threshold with 628 elements. Creating vector time with 628 elements. Creating vector sampleCount with 628 elements. Creating vector time with 628 elements. Creating vector flowCount with 628 elements. Creating vector time with 628 elements. Creating vector flowTime with 628 elements. Creating vector time with 628 elements. Creating vector bufferStatus with 628 elements. Creating vector time with 628 elements. Creating vector laserLevel with 628 elements. Creating vector time with 628 elements. Creating vector counter with 628 elements. Creating vector time with 628 elements. Creating vector counterPeriod with 628 elements. Creating vector time with 628 elements. Creating vector laserControl with 628 elements. Creating vector time with 628 elements. Creating vector countUnknownFrameCharacter with 628 elements. Creating vector time with 628 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 628 elements. Creating vector time with 628 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 628 elements. Creating vector time with 628 elements. Creating vector flowSpeed with 628 elements. Creating vector time with 628 elements. Creating vector countShortLFrameError with 628 elements. Creating vector time with 628 elements. Creating vector countGarbledLFrame with 628 elements. Creating vector time with 628 elements. Creating vector cFrameEsecs with 628 elements. Creating vector time with 628 elements. Creating vector correctedSampleCountList with 628 elements. Creating vector time with 628 elements. Creating vector time with 628 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.04/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.301.04.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_2013.301.04.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 4 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04.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 = 84 Gridding with nix = 252, iZ = 58 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 31099 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 31099 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 10:29 to 10/28/2013 14:30 swr = 262.2445 618.9786 338.2664 347.9576 213.0922 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04_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/2013/2013301/2013.301.04/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013301/2013.301.04/syslog -startEsecs 1382989229.7817 -surveyName Dorado389_2013_301_04_301_04 >> ../results/2013301_GulperTimes.txt Executing: removeGulpDups.py ../results/2013301_GulperTimes.txt Bottle: 0 Time: 1382989574 Depth: 26.7466 Dist: 0.34652 Bottle: 1 Time: 1382990112 Depth: 19.675 Dist: 1.1486 Bottle: 2 Time: 1382991463 Depth: 23.3712 Dist: 3.0223 Bottle: 3 Time: 1382992221 Depth: 10.5827 Dist: 4.012 Bottle: 4 Time: 1382992593 Depth: 3.7567 Dist: 4.5463 Bottle: 5 Time: 1382993161 Depth: 2.7003 Dist: 5.3237 Bottle: 6 Time: 1382993540 Depth: 1.5823 Dist: 5.8513 Bottle: 7 Time: 1382994525 Depth: 6.0414 Dist: 7.1368 Bottle: 8 Time: 1382995079 Depth: 7.7709 Dist: 7.8799 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04_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_301_04_301_04_2column.png Elapsed time to save image: 8 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_301_04_301_04_biolume.png Elapsed time to save image: 28 seconds 2Column contouring gridded variable gLOPCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCtransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCnonTransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCLCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04_lopc.png Elapsed time to save image: 8 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04_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_04_301_04_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_04_301_04_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_04_301_04_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_04_301_04_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_04_301_04_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_04_301_04_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_04_301_04_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_04_301_04_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_04_301_04_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_04_301_04_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_04_301_04_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_04_301_04_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_04_301_04_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_04_301_04_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_04_301_04_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_04_301_04_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_04_301_04_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_04_301_04_Chlorophyll_Fluorescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_04_301_04_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_04_301_04_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_04_301_04_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_04_301_04.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04.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_04_301_04_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_04_301_04.mat ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 5 NaNs found in bbpRed. Interpolating anyway. Encountered 0 NaN values in array of lon that is 2633 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 2633 points from grid Monterey25.grd (2876 x 2447) Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04.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_04_301_04_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... 5 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_04_301_04_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_04_301_04.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_04_301_04_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_04_301_04.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_04_301_04 processed" mccann@mbari.org < mail_Dorado389_2013_301_04_301_04.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.301.04.mat Processing time: 59 seconds