Execution of AUVprocess_main version 1.87 at 2019-02-21T16:28:33Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2018, ['030.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2018.030.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/navigation.nc') Creating vector time with 384008 elements. Creating vector mPos_x with 384008 elements. Creating vector time with 384008 elements. Creating vector mPos_y with 384008 elements. Creating vector time with 384008 elements. Creating vector mDepth with 384008 elements. Creating vector time with 384008 elements. Creating vector mGpsNorth with 384008 elements. Creating vector time with 384008 elements. Creating vector mGpsEast with 384008 elements. Creating vector time with 384008 elements. Creating vector mGpsValid with 384008 elements. Creating vector time with 384008 elements. Creating vector mPhi with 384008 elements. Creating vector time with 384008 elements. Creating vector mTheta with 384008 elements. Creating vector time with 384008 elements. Creating vector mPsi with 384008 elements. Creating vector time with 384008 elements. Creating vector mOmega_x with 384008 elements. Creating vector time with 384008 elements. Creating vector mOmega_y with 384008 elements. Creating vector time with 384008 elements. Creating vector mOmega_z with 384008 elements. Creating vector time with 384008 elements. Creating vector mPsaRange with 384008 elements. Creating vector time with 384008 elements. Creating vector mAltitude with 384008 elements. Creating vector time with 384008 elements. Creating vector multibeamAltitude with 384008 elements. Creating vector time with 384008 elements. Creating vector mDvlAltitude with 384008 elements. Creating vector time with 384008 elements. Creating vector mEchoAltitude with 384008 elements. Creating vector time with 384008 elements. Creating vector mEchoHorizRange with 384008 elements. Creating vector time with 384008 elements. Creating vector mEchoAltitudeLast with 384008 elements. Creating vector time with 384008 elements. Creating vector mEchoHorizRangeLast with 384008 elements. Creating vector time with 384008 elements. Creating vector mEchoNumOfPings with 384008 elements. Creating vector time with 384008 elements. Creating vector nadirCnts with 384008 elements. Creating vector time with 384008 elements. Creating vector obstacleCnts with 384008 elements. Creating vector time with 384008 elements. Creating vector nGoodNadirBeams with 384008 elements. Creating vector time with 384008 elements. Creating vector medianNadirBeamNo with 384008 elements. Creating vector time with 384008 elements. Creating vector mWaterSpeed with 384008 elements. Creating vector time with 384008 elements. Creating vector mDvlValid with 384008 elements. Creating vector time with 384008 elements. Creating vector mDvlNewData with 384008 elements. Creating vector time with 384008 elements. Creating vector mDeltaT with 384008 elements. Creating vector time with 384008 elements. Creating vector nfix with 384008 elements. Creating vector time with 384008 elements. Creating vector efix with 384008 elements. Creating vector time with 384008 elements. Creating vector filter_north with 384008 elements. Creating vector time with 384008 elements. Creating vector filter_east with 384008 elements. Creating vector time with 384008 elements. Creating vector filter_depth with 384008 elements. Creating vector time with 384008 elements. Creating vector north_current with 384008 elements. Creating vector time with 384008 elements. Creating vector east_current with 384008 elements. Creating vector time with 384008 elements. Creating vector speed_bias with 384008 elements. Creating vector time with 384008 elements. Creating vector heading_bias with 384008 elements. Creating vector time with 384008 elements. Creating vector latitude with 384008 elements. Creating vector time with 384008 elements. Creating vector longitude with 384008 elements. Creating vector time with 384008 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/navigation.nc'); [Warning: P-file /mbari/matlab/toolbox/matlab/strfun/num2str.p is older than MATLAB file /mbari/matlab/toolbox/matlab/strfun/num2str.m. /mbari/matlab/toolbox/matlab/strfun/num2str.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In processNav (line 62) In processAUVmission (line 60) In AUVprocess_main (line 225)] processNav(): median of positive valued depths = 32.2228 processNav(): Finding depths less than 225.5599 and times > 0 processNav(): length(Nav.depth) = 384008 processNav(): length(gindx) = 384008 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/2018/2018030/2018.030.00/gps.nc') Creating vector time with 12671 elements. Creating vector hours with 12671 elements. Creating vector time with 12671 elements. Creating vector minutes with 12671 elements. Creating vector time with 12671 elements. Creating vector seconds with 12671 elements. Creating vector time with 12671 elements. Creating vector centiSeconds with 12671 elements. Creating vector time with 12671 elements. Creating vector latitude with 12671 elements. Creating vector time with 12671 elements. Creating vector longitude with 12671 elements. Creating vector time with 12671 elements. Creating vector quality with 12671 elements. Creating vector time with 12671 elements. Creating vector numberOfSatellites with 12671 elements. Creating vector time with 12671 elements. Creating vector hdop with 12671 elements. Creating vector time with 12671 elements. Creating vector antennaHeight with 12671 elements. Creating vector time with 12671 elements. Creating vector geoHeight with 12671 elements. Creating vector time with 12671 elements. Creating vector dgpsDataAge with 12671 elements. Creating vector time with 12671 elements. Creating vector dgpsRSID with 12671 elements. Creating vector time with 12671 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/parosci.nc') Creating vector time with 753898 elements. Creating vector depth with 753898 elements. Creating vector time with 753898 elements. Creating vector temp with 753898 elements. Creating vector time with 753898 elements. Creating vector pressure with 753898 elements. Creating vector time with 753898 elements. Creating vector temp_period with 753898 elements. Creating vector time with 753898 elements. Creating vector pres_period with 753898 elements. Creating vector time with 753898 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.28906 max(Depth.data) = 203.3428 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.28906 max(Depth.data) = 203.3428 [Warning: P-file /mbari/matlab/toolbox/matlab/ops/unique.p is older than MATLAB file /mbari/matlab/toolbox/matlab/ops/unique.m. /mbari/matlab/toolbox/matlab/ops/unique.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In fix_depth_time (line 6) In processDepth (line 65) In processAUVmission (line 106) In AUVprocess_main (line 225)] 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/2018/2018030/2018.030.00/hydroscatlog.nc') Creating vector time with 306010 elements. Creating vector Seconds with 306010 elements. Creating vector time with 306010 elements. Creating vector HundrethsOfSeconds with 306010 elements. Creating vector time with 306010 elements. Creating vector Snorm1 with 306010 elements. Creating vector time with 306010 elements. Creating vector Snorm2 with 306010 elements. Creating vector time with 306010 elements. Creating vector Snorm3 with 306010 elements. Creating vector time with 306010 elements. Creating vector Gain_Status_1 with 306010 elements. Creating vector time with 306010 elements. Creating vector Gain_Status_2 with 306010 elements. Creating vector time with 306010 elements. Creating vector Gain_Status_3 with 306010 elements. Creating vector time with 306010 elements. Creating vector RawDepthValue with 306010 elements. Creating vector time with 306010 elements. Creating vector RawTempValue with 306010 elements. Creating vector time with 306010 elements. Creating vector Temperature with 306010 elements. Creating vector time with 306010 elements. Creating vector ErrorValue with 306010 elements. Creating vector time with 306010 elements. Creating vector bb470 with 306010 elements. Creating vector time with 306010 elements. Creating vector bb676 with 306010 elements. Creating vector time with 306010 elements. Creating vector fl676u with 306010 elements. Creating vector time with 306010 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/ctdDriver.nc') Creating vector time with 306263 elements. Creating vector conductivity with 306263 elements. Creating vector time with 306263 elements. Creating vector temperature with 306263 elements. Creating vector time with 306263 elements. Creating vector cond_frequency with 306263 elements. Creating vector time with 306263 elements. Creating vector temp_frequency with 306263 elements. Creating vector time with 306263 elements. Creating vector spare with 306263 elements. Creating vector time with 306263 elements. Creating vector humidity with 306263 elements. Creating vector time with 306263 elements. Creating vector flow1 with 306263 elements. Creating vector time with 306263 elements. Creating vector CDOM with 306263 elements. Creating vector time with 306263 elements. Creating vector dissolvedO2 with 306263 elements. Creating vector time with 306263 elements. Creating vector salinity with 306263 elements. Creating vector time with 306263 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/ctdDriver2.nc') Creating vector time with 306299 elements. Creating vector conductivity with 306299 elements. Creating vector time with 306299 elements. Creating vector temperature with 306299 elements. Creating vector time with 306299 elements. Creating vector cond_frequency with 306299 elements. Creating vector time with 306299 elements. Creating vector temp_frequency with 306299 elements. Creating vector time with 306299 elements. Creating vector flow2 with 306299 elements. Creating vector time with 306299 elements. Creating vector spare with 306299 elements. Creating vector time with 306299 elements. Creating vector salinity with 306299 elements. Creating vector time with 306299 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/isuslog.nc') Creating vector time with 59838 elements. Creating vector isusNitrate with 59838 elements. Creating vector time with 59838 elements. Creating vector isusTemp with 59838 elements. Creating vector time with 59838 elements. Creating vector isusQuality with 59838 elements. Creating vector time with 59838 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/biolume.nc') Creating vector time with 75528 elements. Creating vector rrr with 75528 elements. Creating vector time with 75528 elements. Creating vector cal_striing with 75528 elements. Creating vector time with 75528 elements. Creating vector avg_biolume with 75528 elements. Creating vector time with 75528 elements. Creating vector pump with 75528 elements. Creating vector time with 75528 elements. Creating vector system_voltage with 75528 elements. Creating vector time with 75528 elements. Creating vector flow with 75528 elements. Creating vector time with 75528 elements. Creating vector HV with 75528 elements. Creating vector time with 75528 elements. Creating vector reserved with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_0 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_1 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_2 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_3 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_4 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_5 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_6 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_7 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_8 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_9 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_10 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_11 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_12 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_13 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_14 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_15 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_16 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_17 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_18 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_19 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_20 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_21 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_22 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_23 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_24 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_25 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_26 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_27 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_28 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_29 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_30 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_31 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_32 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_33 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_34 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_35 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_36 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_37 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_38 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_39 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_40 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_41 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_42 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_43 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_44 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_45 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_46 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_47 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_48 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_49 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_50 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_51 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_52 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_53 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_54 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_55 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_56 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_57 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_58 with 75528 elements. Creating vector time with 75528 elements. Creating vector raw_59 with 75528 elements. Creating vector time with 75528 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/biolume.nc'); Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (7317 x 994) with 7273098 elements. Creating vector time with 7317 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (7317 x 994) with 7273098 elements. Creating vector time with 7317 elements. Creating vector bin with 994 elements. Creating matrix countList (7317 x 994) with 7273098 elements. Creating vector time with 7317 elements. Creating vector bin with 994 elements. Creating vector LCcount with 7317 elements. Creating vector time with 7317 elements. Creating vector transCount with 7317 elements. Creating vector time with 7317 elements. Creating vector nonTransCount with 7317 elements. Creating vector time with 7317 elements. Creating vector ai_mean with 7317 elements. Creating vector time with 7317 elements. Creating vector ai_min with 7317 elements. Creating vector time with 7317 elements. Creating vector ai_max with 7317 elements. Creating vector time with 7317 elements. Creating vector ai_std with 7317 elements. Creating vector time with 7317 elements. Creating vector esd_mean with 7317 elements. Creating vector time with 7317 elements. Creating vector esd_min with 7317 elements. Creating vector time with 7317 elements. Creating vector esd_max with 7317 elements. Creating vector time with 7317 elements. Creating vector esd_std with 7317 elements. Creating vector time with 7317 elements. Creating vector countSum with 7317 elements. Creating vector time with 7317 elements. Creating vector snapshot with 7317 elements. Creating vector time with 7317 elements. Creating vector threshold with 7317 elements. Creating vector time with 7317 elements. Creating vector sampleCount with 7317 elements. Creating vector time with 7317 elements. Creating vector flowCount with 7317 elements. Creating vector time with 7317 elements. Creating vector flowTime with 7317 elements. Creating vector time with 7317 elements. Creating vector bufferStatus with 7317 elements. Creating vector time with 7317 elements. Creating vector laserLevel with 7317 elements. Creating vector time with 7317 elements. Creating vector counter with 7317 elements. Creating vector time with 7317 elements. Creating vector counterPeriod with 7317 elements. Creating vector time with 7317 elements. Creating vector laserControl with 7317 elements. Creating vector time with 7317 elements. Creating vector countUnknownFrameCharacter with 7317 elements. Creating vector time with 7317 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7317 elements. Creating vector time with 7317 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7317 elements. Creating vector time with 7317 elements. Creating vector flowSpeed with 7317 elements. Creating vector time with 7317 elements. Creating vector countShortLFrameError with 7317 elements. Creating vector time with 7317 elements. Creating vector countGarbledLFrame with 7317 elements. Creating vector time with 7317 elements. Creating vector cFrameEsecs with 7317 elements. Creating vector time with 7317 elements. Creating vector correctedSampleCountList with 7317 elements. Creating vector time with 7317 elements. Creating vector time with 7317 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018030/2018.030.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018.030.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Calling build_auv_survey.m to construct survey file... SecondaryDissolvedO2 = [] Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018.030.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 29 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_nav_adjust.png [Warning: P-file /mbari/matlab/toolbox/matlab/imagesci/imformats.p is older than MATLAB file /mbari/matlab/toolbox/matlab/imagesci/imformats.m. /mbari/matlab/toolbox/matlab/imagesci/imformats.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In imwrite>parse_inputs (line 557) In imwrite (line 418) In writeRaster In printingGenerateOutput In alternatePrintPath In print (line 82) In create_data_products (line 99) In build_auv_survey (line 522) In AUVprocess_main (line 255)] [Warning: P-file /mbari/matlab/toolbox/matlab/timefun/datevec.p is older than MATLAB file /mbari/matlab/toolbox/matlab/timefun/datevec.m. /mbari/matlab/toolbox/matlab/timefun/datevec.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In datenum (line 103) In writepng (line 232) In imwrite (line 485) In writeRaster In printingGenerateOutput In alternatePrintPath In print (line 82) In create_data_products (line 99) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00.mat ************************************************************************* Calling plot_sections from ../viz to produce section plots ... Using median boxcar filter of vector... Using mean boxcar filter of vector... Number of profiles found = 418 Gridding with nix = 1254, iZ = 404 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 BL BLflow LOPC count transCount nonTransCount LCcount Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = 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 351358 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 351358 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 120672 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 01/30/2018 08:30 to 01/31/2018 08:30 swr = 108.0387 372.9730 524.6367 538.8052 437.7642 576.9756 457.8651 284.2095 122.6693 10.8277 1.6582 1.7542 1.6164 1.5314 1.1627 1.5830 1.2559 1.4170 1.2000 1.6748 1.4719 1.3281 2.3341 30.7707 169.2171 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2018030_GulperTimes.txt && touch ../results/2018030_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/2018/2018030/2018.030.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2018/2018030/2018.030.00/syslog -startEsecs 1517338553.891 -surveyName Dorado389_2018_030_00_030_00 >> ../results/2018030_GulperTimes.txt Executing: removeGulpDups.py ../results/2018030_GulperTimes.txt Bottle: 0 Time: 1517340229.2862 Depth: 200.0136 Dist: 2.0533 Bottle: 1 Time: 1517340358.8874 Depth: 149.9099 Dist: 2.1954 Bottle: 2 Time: 1517340478.2892 Depth: 99.9389 Dist: 2.3495 Bottle: 3 Time: 1517340533.2854 Depth: 79.9691 Dist: 2.4046 Bottle: 4 Time: 1517340588.8916 Depth: 59.9933 Dist: 2.4712 Bottle: 5 Time: 1517340648.0875 Depth: 39.9684 Dist: 2.5465 Bottle: 6 Time: 1517340687.2848 Depth: 29.9455 Dist: 2.592 Bottle: 7 Time: 1517340722.4924 Depth: 19.9945 Dist: 2.6281 Bottle: 8 Time: 1517340757.2901 Depth: 9.9052 Dist: 2.6615 Bottle: 9 Time: 1517340872.6922 Depth: -0.068843 Dist: 2.7121 Bottle: 10 Time: 1517371711.8895 Depth: 200.0665 Dist: 36.2242 Bottle: 11 Time: 1517371840.6907 Depth: 149.9134 Dist: 36.371 Bottle: 12 Time: 1517371968.092 Depth: 99.9313 Dist: 36.5123 Bottle: 13 Time: 1517372029.6878 Depth: 79.9782 Dist: 36.5753 Bottle: 14 Time: 1517372091.8835 Depth: 59.9029 Dist: 36.6534 Bottle: 15 Time: 1517372155.4891 Depth: 39.9931 Dist: 36.7328 Bottle: 16 Time: 1517372189.4868 Depth: 29.9786 Dist: 36.7665 Bottle: 17 Time: 1517372225.0844 Depth: 19.9811 Dist: 36.8037 Bottle: 18 Time: 1517372260.4919 Depth: 9.9888 Dist: 36.8419 Bottle: 19 Time: 1517372337.8866 Depth: -0.13363 Dist: 36.9062 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_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_2018_030_00_030_00_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/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_biolume.png Elapsed time to save image: 57 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_2018_030_00_030_00_lopc.png Elapsed time to save image: 12 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... [Warning: P-file /mbari/matlab/toolbox/matlab/graph2d/subplot.p is older than MATLAB file /mbari/matlab/toolbox/matlab/graph2d/subplot.m. /mbari/matlab/toolbox/matlab/graph2d/subplot.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In plot_survey_stats (line 47) In create_data_products (line 134) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_2column.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2018/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_2018_030_00_030_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2018/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_2018_030_00_030_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2018/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2018/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_2018_030_00_030_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2018/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_2018_030_00_030_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2018/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_2018_030_00_030_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2018/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_2018_030_00_030_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2018/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_2018_030_00_030_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2018/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2018_030_00_030_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00.kml... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_030_00_030_00_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 420) 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_2018_030_00_030_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 6 NaNs found in bbpBlue. Interpolating anyway. 15 NaNs found in bbpRed. Interpolating anyway. 2 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 5082 NaN values in array of lon that is 59783 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 54701 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 54701 are not equal to number of Lat lon points = 59783 AUV track probably goes outside of the range of the .grd file being used. Setting bottom depths to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00.txt... Copied to /mbari/AUVCTD/surveys/2018/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2018/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 6 NaNs found in bbpBlue. Interpolating anyway. 15 NaNs found in bbpRed. Interpolating anyway. 2 NaNs found in flRed_uncorr. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2018/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_2018_030_00_030_00.nc... Copied to /mbari/AUVCTD/surveys/2018/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2018/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_030_00_030_00.mat... Copied to /mbari/AUVCTD/surveys/2018/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to auvctd@listserver.mbari.org ... !mail -s "Survey Dorado389_2018_030_00_030_00 processed" auvctd@listserver.mbari.org < mail_Dorado389_2018_030_00_030_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018.030.00.mat Processing time: 262 seconds