Execution of AUVprocess_main version 1.88 at 2021-07-29T17:16:11Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2017, ['275.01'], '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: 2017.275.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/ 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/2017/2017275/2017.275.01/navigation.nc') Creating vector time with 406846 elements. Creating vector mPos_x with 406846 elements. Creating vector time with 406846 elements. Creating vector mPos_y with 406846 elements. Creating vector time with 406846 elements. Creating vector mDepth with 406846 elements. Creating vector time with 406846 elements. Creating vector mGpsNorth with 406846 elements. Creating vector time with 406846 elements. Creating vector mGpsEast with 406846 elements. Creating vector time with 406846 elements. Creating vector mGpsValid with 406846 elements. Creating vector time with 406846 elements. Creating vector mPhi with 406846 elements. Creating vector time with 406846 elements. Creating vector mTheta with 406846 elements. Creating vector time with 406846 elements. Creating vector mPsi with 406846 elements. Creating vector time with 406846 elements. Creating vector mOmega_x with 406846 elements. Creating vector time with 406846 elements. Creating vector mOmega_y with 406846 elements. Creating vector time with 406846 elements. Creating vector mOmega_z with 406846 elements. Creating vector time with 406846 elements. Creating vector mPsaRange with 406846 elements. Creating vector time with 406846 elements. Creating vector mAltitude with 406846 elements. Creating vector time with 406846 elements. Creating vector multibeamAltitude with 406846 elements. Creating vector time with 406846 elements. Creating vector mDvlAltitude with 406846 elements. Creating vector time with 406846 elements. Creating vector mEchoAltitude with 406846 elements. Creating vector time with 406846 elements. Creating vector mEchoHorizRange with 406846 elements. Creating vector time with 406846 elements. Creating vector mEchoAltitudeLast with 406846 elements. Creating vector time with 406846 elements. Creating vector mEchoHorizRangeLast with 406846 elements. Creating vector time with 406846 elements. Creating vector mEchoNumOfPings with 406846 elements. Creating vector time with 406846 elements. Creating vector nadirCnts with 406846 elements. Creating vector time with 406846 elements. Creating vector obstacleCnts with 406846 elements. Creating vector time with 406846 elements. Creating vector nGoodNadirBeams with 406846 elements. Creating vector time with 406846 elements. Creating vector medianNadirBeamNo with 406846 elements. Creating vector time with 406846 elements. Creating vector mWaterSpeed with 406846 elements. Creating vector time with 406846 elements. Creating vector mDvlValid with 406846 elements. Creating vector time with 406846 elements. Creating vector mDvlNewData with 406846 elements. Creating vector time with 406846 elements. Creating vector mDeltaT with 406846 elements. Creating vector time with 406846 elements. Creating vector nfix with 406846 elements. Creating vector time with 406846 elements. Creating vector efix with 406846 elements. Creating vector time with 406846 elements. Creating vector filter_north with 406846 elements. Creating vector time with 406846 elements. Creating vector filter_east with 406846 elements. Creating vector time with 406846 elements. Creating vector filter_depth with 406846 elements. Creating vector time with 406846 elements. Creating vector north_current with 406846 elements. Creating vector time with 406846 elements. Creating vector east_current with 406846 elements. Creating vector time with 406846 elements. Creating vector speed_bias with 406846 elements. Creating vector time with 406846 elements. Creating vector heading_bias with 406846 elements. Creating vector time with 406846 elements. Creating vector latitude with 406846 elements. Creating vector time with 406846 elements. Creating vector longitude with 406846 elements. Creating vector time with 406846 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/navigation.nc'); processNav(): median of positive valued depths = 31.6478 processNav(): Finding depths less than 221.5345 and times > 0 processNav(): length(Nav.depth) = 406846 processNav(): length(gindx) = 406846 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/2017/2017275/2017.275.01/gps.nc') Creating vector time with 16353 elements. Creating vector hours with 16353 elements. Creating vector time with 16353 elements. Creating vector minutes with 16353 elements. Creating vector time with 16353 elements. Creating vector seconds with 16353 elements. Creating vector time with 16353 elements. Creating vector centiSeconds with 16353 elements. Creating vector time with 16353 elements. Creating vector latitude with 16353 elements. Creating vector time with 16353 elements. Creating vector longitude with 16353 elements. Creating vector time with 16353 elements. Creating vector quality with 16353 elements. Creating vector time with 16353 elements. Creating vector numberOfSatellites with 16353 elements. Creating vector time with 16353 elements. Creating vector hdop with 16353 elements. Creating vector time with 16353 elements. Creating vector antennaHeight with 16353 elements. Creating vector time with 16353 elements. Creating vector geoHeight with 16353 elements. Creating vector time with 16353 elements. Creating vector dgpsDataAge with 16353 elements. Creating vector time with 16353 elements. Creating vector dgpsRSID with 16353 elements. Creating vector time with 16353 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/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/2017/2017275/2017.275.01/parosci.nc') Creating vector time with 798818 elements. Creating vector depth with 798818 elements. Creating vector time with 798818 elements. Creating vector temp with 798818 elements. Creating vector time with 798818 elements. Creating vector pressure with 798818 elements. Creating vector time with 798818 elements. Creating vector temp_period with 798818 elements. Creating vector time with 798818 elements. Creating vector pres_period with 798818 elements. Creating vector time with 798818 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.31512 max(Depth.data) = 124.7411 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.31512 max(Depth.data) = 124.7411 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/2017/2017275/2017.275.01/hydroscatlog.nc') Creating vector time with 324283 elements. Creating vector Seconds with 324283 elements. Creating vector time with 324283 elements. Creating vector HundrethsOfSeconds with 324283 elements. Creating vector time with 324283 elements. Creating vector Snorm1 with 324283 elements. Creating vector time with 324283 elements. Creating vector Snorm2 with 324283 elements. Creating vector time with 324283 elements. Creating vector Snorm3 with 324283 elements. Creating vector time with 324283 elements. Creating vector Gain_Status_1 with 324283 elements. Creating vector time with 324283 elements. Creating vector Gain_Status_2 with 324283 elements. Creating vector time with 324283 elements. Creating vector Gain_Status_3 with 324283 elements. Creating vector time with 324283 elements. Creating vector RawDepthValue with 324283 elements. Creating vector time with 324283 elements. Creating vector RawTempValue with 324283 elements. Creating vector time with 324283 elements. Creating vector Temperature with 324283 elements. Creating vector time with 324283 elements. Creating vector ErrorValue with 324283 elements. Creating vector time with 324283 elements. Creating vector bb470 with 324283 elements. Creating vector time with 324283 elements. Creating vector bb676 with 324283 elements. Creating vector time with 324283 elements. Creating vector fl676u with 324283 elements. Creating vector time with 324283 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/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/2017/2017275/2017.275.01/ctdDriver.nc') Creating vector time with 324479 elements. Creating vector conductivity with 324479 elements. Creating vector time with 324479 elements. Creating vector temperature with 324479 elements. Creating vector time with 324479 elements. Creating vector cond_frequency with 324479 elements. Creating vector time with 324479 elements. Creating vector temp_frequency with 324479 elements. Creating vector time with 324479 elements. Creating vector spare with 324479 elements. Creating vector time with 324479 elements. Creating vector humidity with 324479 elements. Creating vector time with 324479 elements. Creating vector flow1 with 324479 elements. Creating vector time with 324479 elements. Creating vector CDOM with 324479 elements. Creating vector time with 324479 elements. Creating vector dissolvedO2 with 324479 elements. Creating vector time with 324479 elements. Creating vector salinity with 324479 elements. Creating vector time with 324479 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/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/2017/2017275/2017.275.01/ctdDriver2.nc') Creating vector time with 324464 elements. Creating vector conductivity with 324464 elements. Creating vector time with 324464 elements. Creating vector temperature with 324464 elements. Creating vector time with 324464 elements. Creating vector cond_frequency with 324464 elements. Creating vector time with 324464 elements. Creating vector temp_frequency with 324464 elements. Creating vector time with 324464 elements. Creating vector flow2 with 324464 elements. Creating vector time with 324464 elements. Creating vector spare with 324464 elements. Creating vector time with 324464 elements. Creating vector salinity with 324464 elements. Creating vector time with 324464 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/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/2017/2017275/2017.275.01/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/2017/2017275/2017.275.01/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/2017/2017275/2017.275.01/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/2017/2017275/2017.275.01/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/2017/2017275/2017.275.01/biolume.nc') Creating vector time with 80028 elements. Creating vector rrr with 80028 elements. Creating vector time with 80028 elements. Creating vector cal_striing with 80028 elements. Creating vector time with 80028 elements. Creating vector avg_biolume with 80028 elements. Creating vector time with 80028 elements. Creating vector pump with 80028 elements. Creating vector time with 80028 elements. Creating vector system_voltage with 80028 elements. Creating vector time with 80028 elements. Creating vector flow with 80028 elements. Creating vector time with 80028 elements. Creating vector HV with 80028 elements. Creating vector time with 80028 elements. Creating vector reserved with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_0 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_1 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_2 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_3 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_4 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_5 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_6 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_7 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_8 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_9 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_10 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_11 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_12 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_13 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_14 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_15 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_16 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_17 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_18 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_19 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_20 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_21 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_22 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_23 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_24 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_25 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_26 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_27 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_28 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_29 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_30 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_31 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_32 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_33 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_34 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_35 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_36 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_37 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_38 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_39 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_40 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_41 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_42 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_43 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_44 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_45 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_46 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_47 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_48 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_49 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_50 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_51 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_52 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_53 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_54 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_55 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_56 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_57 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_58 with 80028 elements. Creating vector time with 80028 elements. Creating vector raw_59 with 80028 elements. Creating vector time with 80028 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/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/2017/2017275/2017.275.01/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (7588 x 994) with 7542472 elements. Creating vector time with 7588 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (7588 x 994) with 7542472 elements. Creating vector time with 7588 elements. Creating vector bin with 994 elements. Creating matrix countList (7588 x 994) with 7542472 elements. Creating vector time with 7588 elements. Creating vector bin with 994 elements. Creating vector LCcount with 7588 elements. Creating vector time with 7588 elements. Creating vector transCount with 7588 elements. Creating vector time with 7588 elements. Creating vector nonTransCount with 7588 elements. Creating vector time with 7588 elements. Creating vector ai_mean with 7588 elements. Creating vector time with 7588 elements. Creating vector ai_min with 7588 elements. Creating vector time with 7588 elements. Creating vector ai_max with 7588 elements. Creating vector time with 7588 elements. Creating vector ai_std with 7588 elements. Creating vector time with 7588 elements. Creating vector esd_mean with 7588 elements. Creating vector time with 7588 elements. Creating vector esd_min with 7588 elements. Creating vector time with 7588 elements. Creating vector esd_max with 7588 elements. Creating vector time with 7588 elements. Creating vector esd_std with 7588 elements. Creating vector time with 7588 elements. Creating vector countSum with 7588 elements. Creating vector time with 7588 elements. Creating vector snapshot with 7588 elements. Creating vector time with 7588 elements. Creating vector threshold with 7588 elements. Creating vector time with 7588 elements. Creating vector sampleCount with 7588 elements. Creating vector time with 7588 elements. Creating vector flowCount with 7588 elements. Creating vector time with 7588 elements. Creating vector flowTime with 7588 elements. Creating vector time with 7588 elements. Creating vector bufferStatus with 7588 elements. Creating vector time with 7588 elements. Creating vector laserLevel with 7588 elements. Creating vector time with 7588 elements. Creating vector counter with 7588 elements. Creating vector time with 7588 elements. Creating vector counterPeriod with 7588 elements. Creating vector time with 7588 elements. Creating vector laserControl with 7588 elements. Creating vector time with 7588 elements. Creating vector countUnknownFrameCharacter with 7588 elements. Creating vector time with 7588 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7588 elements. Creating vector time with 7588 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7588 elements. Creating vector time with 7588 elements. Creating vector flowSpeed with 7588 elements. Creating vector time with 7588 elements. Creating vector countShortLFrameError with 7588 elements. Creating vector time with 7588 elements. Creating vector countGarbledLFrame with 7588 elements. Creating vector time with 7588 elements. Creating vector cFrameEsecs with 7588 elements. Creating vector time with 7588 elements. Creating vector correctedSampleCountList with 7588 elements. Creating vector time with 7588 elements. Creating vector time with 7588 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017275/2017.275.01/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017.275.01.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_2017.275.01.mat has_par2 = 0 Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 22 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_275_01_275_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_275_01_275_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_275_01_275_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 = 384 Gridding with nix = 1152, iZ = 245 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 326287 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 326287 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: 10/02/2017 10:29 to 10/03/2017 10:29 swr = 670.3013 773.3680 802.8449 783.9636 658.1124 538.6370 360.7086 179.6667 33.0248 1.5914 1.6667 1.6580 1.3957 1.6377 1.6537 1.5056 2.0858 1.2593 1.6333 2.0709 2.1531 48.3650 238.7382 412.0172 600.1759 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_275_01_275_01_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2017275_GulperTimes.txt && touch ../results/2017275_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/2017/2017275/2017.275.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2017/2017275/2017.275.01/syslog -startEsecs 1506970823.0493 -surveyName Dorado389_2017_275_01_275_01 >> ../results/2017275_GulperTimes.txt Executing: removeGulpDups.py ../results/2017275_GulperTimes.txt Bottle: 0 Time: 1506975389.8465 Depth: 32.5762 Dist: 5.1667 Bottle: 1 Time: 1506975395.2461 Depth: 34.8498 Dist: 5.1716 Bottle: 2 Time: 1506975400.4457 Depth: 36.1082 Dist: 5.1764 Bottle: 3 Time: 1506975405.6454 Depth: 36.2056 Dist: 5.1812 Bottle: 4 Time: 1506975410.855 Depth: 35.7774 Dist: 5.1859 Bottle: 5 Time: 1506975416.0447 Depth: 35.4117 Dist: 5.1907 Bottle: 6 Time: 1506975455.242 Depth: 29.965 Dist: 5.2293 Bottle: 7 Time: 1506975495.4492 Depth: 19.9391 Dist: 5.2768 Bottle: 8 Time: 1506975529.8469 Depth: 9.8931 Dist: 5.3165 Bottle: 9 Time: 1506975599.4421 Depth: 0.0073248 Dist: 5.3783 Bottle: 10 Time: 1507009632.4507 Depth: -0.046256 Dist: 38.5512 Bottle: 11 Time: 1507009699.8461 Depth: 10.0604 Dist: 38.6106 Bottle: 12 Time: 1507009734.8437 Depth: 20.0509 Dist: 38.6507 Bottle: 13 Time: 1507009777.6507 Depth: 30.029 Dist: 38.6912 Bottle: 14 Time: 1507009818.048 Depth: 40.0689 Dist: 38.7381 Bottle: 15 Time: 1507009889.643 Depth: 60.0342 Dist: 38.8261 Bottle: 16 Time: 1507009957.0484 Depth: 80.008 Dist: 38.8975 Bottle: 17 Time: 1507010026.6437 Depth: 100.0337 Dist: 38.988 Bottle: 18 Time: 1507010271.8469 Depth: 103.669 Dist: 39.1142 Bottle: 19 Time: 1507010517.0501 Depth: 110.807 Dist: 39.2395 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_275_01_275_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_275_01_275_01_2column.png Elapsed time to save image: 12 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_275_01_275_01_biolume.png Elapsed time to save image: 46 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_275_01_275_01_lopc.png Elapsed time to save image: 12 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_275_01_275_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_275_01_275_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_275_01_275_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_275_01_275_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_275_01_275_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_275_01_275_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_275_01_275_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_275_01_275_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) = 2017-10-02T19:00:23Z gmtstr(tend) = 2017-10-03T17:36:32Z Interpolating ctd2 temperature... Interpolating ctd2 salinity... 18 NaNs found in bbpBlue. Interpolating anyway. 116 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_275_01_275_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_01_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_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. adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_01_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_01_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_01_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_01_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_01_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_01_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_01_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_275_01_275_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_275_01_275_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_275_01_275_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_275_01_275_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_275_01_275_01.mat ... Iterpolating to 2 second increments between Nav time bounds... gmtstr(tstart) = 2017-10-02T19:00:23Z gmtstr(tend) = 2017-10-03T17:36:32Z Interpolating ctd2 temperature... Interpolating ctd2 salinity... 18 NaNs found in bbpBlue. Interpolating anyway. 116 NaNs found in bbpRed. Interpolating anyway. 3 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 8057 NaN values in array of lon that is 40685 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 32628 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 32628 are not equal to number of Lat lon points = 40685 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_275_01_275_01.txt Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_275_01_275_01_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_275_01_275_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_275_01_275_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_275_01_275_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_275_01_275_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_275_01_275_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_275_01_275_01.nc ************************************************************************* Composing email to send to auvctd@listserver.mbari.org ... !mail -s "Survey Dorado389_2017_275_01_275_01 processed" auvctd@listserver.mbari.org < mail_Dorado389_2017_275_01_275_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017.275.01.mat Processing time: 242 seconds