Execution of AUVprocess_main version 1.88 at 2021-07-29T17:06:58Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2017, ['248.01'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd2') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2017.248.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd.cvs/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/2017/2017248/2017.248.01/navigation.nc') Creating vector time with 423699 elements. Creating vector mPos_x with 423699 elements. Creating vector time with 423699 elements. Creating vector mPos_y with 423699 elements. Creating vector time with 423699 elements. Creating vector mDepth with 423699 elements. Creating vector time with 423699 elements. Creating vector mGpsNorth with 423699 elements. Creating vector time with 423699 elements. Creating vector mGpsEast with 423699 elements. Creating vector time with 423699 elements. Creating vector mGpsValid with 423699 elements. Creating vector time with 423699 elements. Creating vector mPhi with 423699 elements. Creating vector time with 423699 elements. Creating vector mTheta with 423699 elements. Creating vector time with 423699 elements. Creating vector mPsi with 423699 elements. Creating vector time with 423699 elements. Creating vector mOmega_x with 423699 elements. Creating vector time with 423699 elements. Creating vector mOmega_y with 423699 elements. Creating vector time with 423699 elements. Creating vector mOmega_z with 423699 elements. Creating vector time with 423699 elements. Creating vector mPsaRange with 423699 elements. Creating vector time with 423699 elements. Creating vector mAltitude with 423699 elements. Creating vector time with 423699 elements. Creating vector multibeamAltitude with 423699 elements. Creating vector time with 423699 elements. Creating vector mDvlAltitude with 423699 elements. Creating vector time with 423699 elements. Creating vector mEchoAltitude with 423699 elements. Creating vector time with 423699 elements. Creating vector mEchoHorizRange with 423699 elements. Creating vector time with 423699 elements. Creating vector mEchoAltitudeLast with 423699 elements. Creating vector time with 423699 elements. Creating vector mEchoHorizRangeLast with 423699 elements. Creating vector time with 423699 elements. Creating vector mEchoNumOfPings with 423699 elements. Creating vector time with 423699 elements. Creating vector nadirCnts with 423699 elements. Creating vector time with 423699 elements. Creating vector obstacleCnts with 423699 elements. Creating vector time with 423699 elements. Creating vector nGoodNadirBeams with 423699 elements. Creating vector time with 423699 elements. Creating vector medianNadirBeamNo with 423699 elements. Creating vector time with 423699 elements. Creating vector mWaterSpeed with 423699 elements. Creating vector time with 423699 elements. Creating vector mDvlValid with 423699 elements. Creating vector time with 423699 elements. Creating vector mDvlNewData with 423699 elements. Creating vector time with 423699 elements. Creating vector mDeltaT with 423699 elements. Creating vector time with 423699 elements. Creating vector nfix with 423699 elements. Creating vector time with 423699 elements. Creating vector efix with 423699 elements. Creating vector time with 423699 elements. Creating vector filter_north with 423699 elements. Creating vector time with 423699 elements. Creating vector filter_east with 423699 elements. Creating vector time with 423699 elements. Creating vector filter_depth with 423699 elements. Creating vector time with 423699 elements. Creating vector north_current with 423699 elements. Creating vector time with 423699 elements. Creating vector east_current with 423699 elements. Creating vector time with 423699 elements. Creating vector speed_bias with 423699 elements. Creating vector time with 423699 elements. Creating vector heading_bias with 423699 elements. Creating vector time with 423699 elements. Creating vector latitude with 423699 elements. Creating vector time with 423699 elements. Creating vector longitude with 423699 elements. Creating vector time with 423699 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/navigation.nc'); processNav(): median of positive valued depths = 30.9959 processNav(): Finding depths less than 216.9714 and times > 0 processNav(): length(Nav.depth) = 423699 processNav(): length(gindx) = 423699 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/2017/2017248/2017.248.01/gps.nc') Creating vector time with 12412 elements. Creating vector hours with 12412 elements. Creating vector time with 12412 elements. Creating vector minutes with 12412 elements. Creating vector time with 12412 elements. Creating vector seconds with 12412 elements. Creating vector time with 12412 elements. Creating vector centiSeconds with 12412 elements. Creating vector time with 12412 elements. Creating vector latitude with 12412 elements. Creating vector time with 12412 elements. Creating vector longitude with 12412 elements. Creating vector time with 12412 elements. Creating vector quality with 12412 elements. Creating vector time with 12412 elements. Creating vector numberOfSatellites with 12412 elements. Creating vector time with 12412 elements. Creating vector hdop with 12412 elements. Creating vector time with 12412 elements. Creating vector antennaHeight with 12412 elements. Creating vector time with 12412 elements. Creating vector geoHeight with 12412 elements. Creating vector time with 12412 elements. Creating vector dgpsDataAge with 12412 elements. Creating vector time with 12412 elements. Creating vector dgpsRSID with 12412 elements. Creating vector time with 12412 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/parosci.nc') Creating vector time with 831803 elements. Creating vector depth with 831803 elements. Creating vector time with 831803 elements. Creating vector temp with 831803 elements. Creating vector time with 831803 elements. Creating vector pressure with 831803 elements. Creating vector time with 831803 elements. Creating vector temp_period with 831803 elements. Creating vector time with 831803 elements. Creating vector pres_period with 831803 elements. Creating vector time with 831803 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.37803 max(Depth.data) = 102.3278 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.37803 max(Depth.data) = 102.3278 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/2017/2017248/2017.248.01/hydroscatlog.nc') Creating vector time with 336451 elements. Creating vector Seconds with 336451 elements. Creating vector time with 336451 elements. Creating vector HundrethsOfSeconds with 336451 elements. Creating vector time with 336451 elements. Creating vector Snorm1 with 336451 elements. Creating vector time with 336451 elements. Creating vector Snorm2 with 336451 elements. Creating vector time with 336451 elements. Creating vector Snorm3 with 336451 elements. Creating vector time with 336451 elements. Creating vector Gain_Status_1 with 336451 elements. Creating vector time with 336451 elements. Creating vector Gain_Status_2 with 336451 elements. Creating vector time with 336451 elements. Creating vector Gain_Status_3 with 336451 elements. Creating vector time with 336451 elements. Creating vector RawDepthValue with 336451 elements. Creating vector time with 336451 elements. Creating vector RawTempValue with 336451 elements. Creating vector time with 336451 elements. Creating vector Temperature with 336451 elements. Creating vector time with 336451 elements. Creating vector ErrorValue with 336451 elements. Creating vector time with 336451 elements. Creating vector bb470 with 336451 elements. Creating vector time with 336451 elements. Creating vector bb676 with 336451 elements. Creating vector time with 336451 elements. Creating vector fl676u with 336451 elements. Creating vector time with 336451 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/ctdDriver.nc') Creating vector time with 336888 elements. Creating vector conductivity with 336888 elements. Creating vector time with 336888 elements. Creating vector temperature with 336888 elements. Creating vector time with 336888 elements. Creating vector cond_frequency with 336888 elements. Creating vector time with 336888 elements. Creating vector temp_frequency with 336888 elements. Creating vector time with 336888 elements. Creating vector spare with 336888 elements. Creating vector time with 336888 elements. Creating vector humidity with 336888 elements. Creating vector time with 336888 elements. Creating vector flow1 with 336888 elements. Creating vector time with 336888 elements. Creating vector CDOM with 336888 elements. Creating vector time with 336888 elements. Creating vector dissolvedO2 with 336888 elements. Creating vector time with 336888 elements. Creating vector salinity with 336888 elements. Creating vector time with 336888 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/ctdDriver2.nc') Creating vector time with 336827 elements. Creating vector conductivity with 336827 elements. Creating vector time with 336827 elements. Creating vector temperature with 336827 elements. Creating vector time with 336827 elements. Creating vector cond_frequency with 336827 elements. Creating vector time with 336827 elements. Creating vector temp_frequency with 336827 elements. Creating vector time with 336827 elements. Creating vector flow2 with 336827 elements. Creating vector time with 336827 elements. Creating vector spare with 336827 elements. Creating vector time with 336827 elements. Creating vector salinity with 336827 elements. Creating vector time with 336827 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/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/2017/2017248/2017.248.01/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/2017/2017248/2017.248.01/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/2017/2017248/2017.248.01/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 71) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 227)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 71) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 227)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/biolume.nc') Creating vector time with 83292 elements. Creating vector rrr with 83292 elements. Creating vector time with 83292 elements. Creating vector cal_striing with 83292 elements. Creating vector time with 83292 elements. Creating vector avg_biolume with 83292 elements. Creating vector time with 83292 elements. Creating vector pump with 83292 elements. Creating vector time with 83292 elements. Creating vector system_voltage with 83292 elements. Creating vector time with 83292 elements. Creating vector flow with 83292 elements. Creating vector time with 83292 elements. Creating vector HV with 83292 elements. Creating vector time with 83292 elements. Creating vector reserved with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_0 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_1 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_2 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_3 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_4 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_5 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_6 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_7 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_8 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_9 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_10 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_11 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_12 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_13 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_14 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_15 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_16 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_17 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_18 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_19 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_20 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_21 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_22 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_23 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_24 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_25 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_26 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_27 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_28 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_29 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_30 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_31 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_32 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_33 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_34 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_35 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_36 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_37 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_38 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_39 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_40 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_41 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_42 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_43 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_44 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_45 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_46 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_47 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_48 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_49 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_50 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_51 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_52 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_53 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_54 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_55 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_56 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_57 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_58 with 83292 elements. Creating vector time with 83292 elements. Creating vector raw_59 with 83292 elements. Creating vector time with 83292 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/biolume.nc'); Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (8021 x 994) with 7972874 elements. Creating vector time with 8021 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (8021 x 994) with 7972874 elements. Creating vector time with 8021 elements. Creating vector bin with 994 elements. Creating matrix countList (8021 x 994) with 7972874 elements. Creating vector time with 8021 elements. Creating vector bin with 994 elements. Creating vector LCcount with 8021 elements. Creating vector time with 8021 elements. Creating vector transCount with 8021 elements. Creating vector time with 8021 elements. Creating vector nonTransCount with 8021 elements. Creating vector time with 8021 elements. Creating vector ai_mean with 8021 elements. Creating vector time with 8021 elements. Creating vector ai_min with 8021 elements. Creating vector time with 8021 elements. Creating vector ai_max with 8021 elements. Creating vector time with 8021 elements. Creating vector ai_std with 8021 elements. Creating vector time with 8021 elements. Creating vector esd_mean with 8021 elements. Creating vector time with 8021 elements. Creating vector esd_min with 8021 elements. Creating vector time with 8021 elements. Creating vector esd_max with 8021 elements. Creating vector time with 8021 elements. Creating vector esd_std with 8021 elements. Creating vector time with 8021 elements. Creating vector countSum with 8021 elements. Creating vector time with 8021 elements. Creating vector snapshot with 8021 elements. Creating vector time with 8021 elements. Creating vector threshold with 8021 elements. Creating vector time with 8021 elements. Creating vector sampleCount with 8021 elements. Creating vector time with 8021 elements. Creating vector flowCount with 8021 elements. Creating vector time with 8021 elements. Creating vector flowTime with 8021 elements. Creating vector time with 8021 elements. Creating vector bufferStatus with 8021 elements. Creating vector time with 8021 elements. Creating vector laserLevel with 8021 elements. Creating vector time with 8021 elements. Creating vector counter with 8021 elements. Creating vector time with 8021 elements. Creating vector counterPeriod with 8021 elements. Creating vector time with 8021 elements. Creating vector laserControl with 8021 elements. Creating vector time with 8021 elements. Creating vector countUnknownFrameCharacter with 8021 elements. Creating vector time with 8021 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 8021 elements. Creating vector time with 8021 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 8021 elements. Creating vector time with 8021 elements. Creating vector flowSpeed with 8021 elements. Creating vector time with 8021 elements. Creating vector countShortLFrameError with 8021 elements. Creating vector time with 8021 elements. Creating vector countGarbledLFrame with 8021 elements. Creating vector time with 8021 elements. Creating vector cFrameEsecs with 8021 elements. Creating vector time with 8021 elements. Creating vector correctedSampleCountList with 8021 elements. Creating vector time with 8021 elements. Creating vector time with 8021 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017248/2017.248.01/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017.248.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Calling build_auv_survey.m to construct survey file... SecondaryDissolvedO2 = [] Reading: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017.248.01.mat has_par2 = 0 Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 30 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01.mat ************************************************************************* Calling plot_sections from ../viz to produce section plots ... Using median boxcar filter of vector... Using mean boxcar filter of vector... Number of profiles found = 446 Gridding with nix = 1338, iZ = 202 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 count transCount nonTransCount LCcount 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 cvarname = gLOPCtransCount cvarname = gLOPCnonTransCount cvarname = gLOPCLCcount Encountered 0 NaN values in array of lon that is 420237 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 420237 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 145548 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 09/05/2017 12:30 to 09/06/2017 14:30 swr = 812.5751 845.6962 605.0061 346.8848 280.1136 237.3397 77.8277 3.7637 1.1331 0.8334 1.1001 1.1334 1.2666 1.2331 1.2002 1.2335 1.3329 1.2335 2.0472 18.0181 52.1534 NaN NaN 406.9698 384.1466 545.9279 501.3501 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2017248_GulperTimes.txt && touch ../results/2017248_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/2017/2017248/2017.248.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2017/2017248/2017.248.01/syslog -startEsecs 1504646905.7375 -surveyName Dorado389_2017_248_01_248_01 >> ../results/2017248_GulperTimes.txt Executing: removeGulpDups.py ../results/2017248_GulperTimes.txt Bottle: 0 Time: 1504653267.46 Depth: 1.6053 Dist: 6.8377 Bottle: 1 Time: 1504655673.87 Depth: 12.3372 Dist: 8.7396 Bottle: 2 Time: 1504658080.66 Depth: 15.8216 Dist: 10.892 Bottle: 3 Time: 1504670760.26 Depth: 8.1152 Dist: 23.9689 Bottle: 4 Time: 1504672773.27 Depth: 10.5493 Dist: 25.7254 Bottle: 5 Time: 1504676110.27 Depth: 11.936 Dist: 28.6361 Bottle: 6 Time: 1504688294.3422 Depth: -0.10459 Dist: 39.9001 Bottle: 7 Time: 1504688390.5356 Depth: 20.0178 Dist: 40.0067 Bottle: 8 Time: 1504688457.331 Depth: 40.0029 Dist: 40.0847 Bottle: 9 Time: 1504688531.7359 Depth: 60.0894 Dist: 40.1749 Bottle: 10 Time: 1504690860.07 Depth: 7.1605 Dist: 42.37 Bottle: 11 Time: 1504693368.46 Depth: 9.5504 Dist: 44.7247 Bottle: 12 Time: 1504696093.07 Depth: 11.4366 Dist: 47.2928 Bottle: 13 Time: 1504709755.26 Depth: 2.683 Dist: 58.781 Bottle: 14 Time: 1504712781.06 Depth: 8.0929 Dist: 60.8194 Bottle: 15 Time: 1504715439.26 Depth: 4.6071 Dist: 63.3954 Bottle: 16 Time: 1504728366.1371 Depth: -0.11156 Dist: 74.8636 Bottle: 17 Time: 1504728476.9395 Depth: 20.037 Dist: 74.9674 Bottle: 18 Time: 1504728543.3349 Depth: 40.0233 Dist: 75.046 Bottle: 19 Time: 1504728612.5302 Depth: 60.0293 Dist: 75.1267 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_gridded.mat outvarstr = 'gF gT gN gS gD gO gB420 gB700 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth ' 2Column contouring gridded variable gD Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gS Drawing bottom contour from EM300 data 2Column contouring gridded variable gN Drawing bottom contour from EM300 data 2Column contouring gridded variable gO Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_2column.png Elapsed time to save image: 18 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.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_biolume.png Elapsed time to save image: 45 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.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_lopc.png Elapsed time to save image: 14 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_2column.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_biolume.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_lopc.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to 2 second increments between Nav time bounds... gmtstr(tstart) = 2017-09-05T21:28:25Z gmtstr(tend) = 2017-09-06T21:00:45Z Interpolating ctd2 temperature... Interpolating ctd2 salinity... 1 NaNs found in bbpBlue. Interpolating anyway. 4 NaNs found in bbpRed. Interpolating anyway. 3 NaNs found in flRed_uncorr. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_decim.nc... Copied to /mbari/AUVCTD/surveys/2017/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Creating Dorado389_2017_248_01_248_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01.kml... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_248_01_248_01_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 445) In build_auv_survey (line 530) In AUVprocess_main (line 257)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01.mat ... Iterpolating to 2 second increments between Nav time bounds... gmtstr(tstart) = 2017-09-05T21:28:25Z gmtstr(tend) = 2017-09-06T21:00:45Z Interpolating ctd2 temperature... Interpolating ctd2 salinity... 1 NaNs found in bbpBlue. Interpolating anyway. 4 NaNs found in bbpRed. Interpolating anyway. 3 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 347 NaN values in array of lon that is 42370 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 42023 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 42023 are not equal to number of Lat lon points = 42370 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.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01.txt Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01.txt... Copied to /mbari/AUVCTD/surveys/2017/odv/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2017/odv/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01.nc... Copied to /mbari/AUVCTD/surveys/2017/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01_gridded.mat... Copied to /mbari/AUVCTD/surveys/2017/mat/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_248_01_248_01.mat... Copied to /mbari/AUVCTD/surveys/2017/mat/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ permalink_url.sh http://dods.mbari.org/cgi-bin/nph-nc/data/auvctd/surveys/2017/netcdf/Dorado389_2017_248_01_248_01.nc ************************************************************************* Composing email to send to auvctd@listserver.mbari.org ... !mail -s "Survey Dorado389_2017_248_01_248_01 processed" auvctd@listserver.mbari.org < mail_Dorado389_2017_248_01_248_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017.248.01.mat Processing time: 361 seconds