Execution of AUVprocess_main version 1.86 at 2018-05-23T23:45:39Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2011, ['111.00'], '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: 2011.111.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/ 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/2011/2011111/2011.111.00/navigation.nc') Creating vector time with 307221 elements. Creating vector mPos_x with 307221 elements. Creating vector time with 307221 elements. Creating vector mPos_y with 307221 elements. Creating vector time with 307221 elements. Creating vector mDepth with 307221 elements. Creating vector time with 307221 elements. Creating vector mGpsNorth with 307221 elements. Creating vector time with 307221 elements. Creating vector mGpsEast with 307221 elements. Creating vector time with 307221 elements. Creating vector mGpsValid with 307221 elements. Creating vector time with 307221 elements. Creating vector mPhi with 307221 elements. Creating vector time with 307221 elements. Creating vector mTheta with 307221 elements. Creating vector time with 307221 elements. Creating vector mPsi with 307221 elements. Creating vector time with 307221 elements. Creating vector mOmega_x with 307221 elements. Creating vector time with 307221 elements. Creating vector mOmega_y with 307221 elements. Creating vector time with 307221 elements. Creating vector mOmega_z with 307221 elements. Creating vector time with 307221 elements. Creating vector mPsaRange with 307221 elements. Creating vector time with 307221 elements. Creating vector mAltitude with 307221 elements. Creating vector time with 307221 elements. Creating vector mDvlAltitude with 307221 elements. Creating vector time with 307221 elements. Creating vector mEchoAltitude with 307221 elements. Creating vector time with 307221 elements. Creating vector mEchoHorizRange with 307221 elements. Creating vector time with 307221 elements. Creating vector mEchoAltitudeLast with 307221 elements. Creating vector time with 307221 elements. Creating vector mEchoHorizRangeLast with 307221 elements. Creating vector time with 307221 elements. Creating vector mEchoNumOfPings with 307221 elements. Creating vector time with 307221 elements. Creating vector mWaterSpeed with 307221 elements. Creating vector time with 307221 elements. Creating vector mDvlValid with 307221 elements. Creating vector time with 307221 elements. Creating vector mDvlNewData with 307221 elements. Creating vector time with 307221 elements. Creating vector mDeltaT with 307221 elements. Creating vector time with 307221 elements. Creating vector nfix with 307221 elements. Creating vector time with 307221 elements. Creating vector efix with 307221 elements. Creating vector time with 307221 elements. Creating vector filter_north with 307221 elements. Creating vector time with 307221 elements. Creating vector filter_east with 307221 elements. Creating vector time with 307221 elements. Creating vector filter_depth with 307221 elements. Creating vector time with 307221 elements. Creating vector north_current with 307221 elements. Creating vector time with 307221 elements. Creating vector east_current with 307221 elements. Creating vector time with 307221 elements. Creating vector speed_bias with 307221 elements. Creating vector time with 307221 elements. Creating vector heading_bias with 307221 elements. Creating vector time with 307221 elements. Creating vector latitude with 307221 elements. Creating vector time with 307221 elements. Creating vector longitude with 307221 elements. Creating vector time with 307221 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/navigation.nc'); processNav(): median of positive valued depths = 20.3704 processNav(): Finding depths less than 142.5931 and times > 0 processNav(): length(Nav.depth) = 307221 processNav(): length(gindx) = 307221 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/2011/2011111/2011.111.00/gps.nc') Creating vector time with 14051 elements. Creating vector hours with 14051 elements. Creating vector time with 14051 elements. Creating vector minutes with 14051 elements. Creating vector time with 14051 elements. Creating vector seconds with 14051 elements. Creating vector time with 14051 elements. Creating vector centiSeconds with 14051 elements. Creating vector time with 14051 elements. Creating vector latitude with 14051 elements. Creating vector time with 14051 elements. Creating vector longitude with 14051 elements. Creating vector time with 14051 elements. Creating vector quality with 14051 elements. Creating vector time with 14051 elements. Creating vector numberOfSatellites with 14051 elements. Creating vector time with 14051 elements. Creating vector hdop with 14051 elements. Creating vector time with 14051 elements. Creating vector antennaHeight with 14051 elements. Creating vector time with 14051 elements. Creating vector geoHeight with 14051 elements. Creating vector time with 14051 elements. Creating vector dgpsDataAge with 14051 elements. Creating vector time with 14051 elements. Creating vector dgpsRSID with 14051 elements. Creating vector time with 14051 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/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/2011/2011111/2011.111.00/parosci.nc') Creating vector time with 520884 elements. Creating vector depth with 520884 elements. Creating vector time with 520884 elements. Creating vector temp with 520884 elements. Creating vector time with 520884 elements. Creating vector pressure with 520884 elements. Creating vector time with 520884 elements. Creating vector temp_period with 520884 elements. Creating vector time with 520884 elements. Creating vector pres_period with 520884 elements. Creating vector time with 520884 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.62287 max(Depth.data) = 40.3035 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.62287 max(Depth.data) = 40.3035 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/2011/2011111/2011.111.00/hydroscatlog.nc') Creating vector time with 245763 elements. Creating vector Seconds with 245763 elements. Creating vector time with 245763 elements. Creating vector HundrethsOfSeconds with 245763 elements. Creating vector time with 245763 elements. Creating vector Snorm1 with 245763 elements. Creating vector time with 245763 elements. Creating vector Snorm2 with 245763 elements. Creating vector time with 245763 elements. Creating vector Snorm3 with 245763 elements. Creating vector time with 245763 elements. Creating vector Gain_Status_1 with 245763 elements. Creating vector time with 245763 elements. Creating vector Gain_Status_2 with 245763 elements. Creating vector time with 245763 elements. Creating vector Gain_Status_3 with 245763 elements. Creating vector time with 245763 elements. Creating vector RawDepthValue with 245763 elements. Creating vector time with 245763 elements. Creating vector RawTempValue with 245763 elements. Creating vector time with 245763 elements. Creating vector Temperature with 245763 elements. Creating vector time with 245763 elements. Creating vector ErrorValue with 245763 elements. Creating vector time with 245763 elements. Creating vector bb470 with 245763 elements. Creating vector time with 245763 elements. Creating vector bb676 with 245763 elements. Creating vector time with 245763 elements. Creating vector fl676u with 245763 elements. Creating vector time with 245763 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/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/2011/2011111/2011.111.00/ctdDriver.nc') Creating vector time with 245828 elements. Creating vector conductivity with 245828 elements. Creating vector time with 245828 elements. Creating vector temperature with 245828 elements. Creating vector time with 245828 elements. Creating vector cond_frequency with 245828 elements. Creating vector time with 245828 elements. Creating vector temp_frequency with 245828 elements. Creating vector time with 245828 elements. Creating vector spare with 245828 elements. Creating vector time with 245828 elements. Creating vector humidity with 245828 elements. Creating vector time with 245828 elements. Creating vector flow1 with 245828 elements. Creating vector time with 245828 elements. Creating vector rhodamine with 245828 elements. Creating vector time with 245828 elements. Creating vector dissolvedO2 with 245828 elements. Creating vector time with 245828 elements. Creating vector salinity with 245828 elements. Creating vector time with 245828 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/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/2011/2011111/2011.111.00/ctdDriver2.nc') Creating vector time with 245827 elements. Creating vector conductivity with 245827 elements. Creating vector time with 245827 elements. Creating vector temperature with 245827 elements. Creating vector time with 245827 elements. Creating vector cond_frequency with 245827 elements. Creating vector time with 245827 elements. Creating vector temp_frequency with 245827 elements. Creating vector time with 245827 elements. Creating vector flow2 with 245827 elements. Creating vector time with 245827 elements. Creating vector spare with 245827 elements. Creating vector time with 245827 elements. Creating vector salinity with 245827 elements. Creating vector time with 245827 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/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/2011/2011111/2011.111.00/isuslog.nc') Creating vector time with 47702 elements. Creating vector isusNitrate with 47702 elements. Creating vector time with 47702 elements. Creating vector isusTemp with 47702 elements. Creating vector time with 47702 elements. Creating vector isusQuality with 47702 elements. Creating vector time with 47702 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/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/2011/2011111/2011.111.00/biolume.nc') Creating vector time with 60451 elements. Creating vector rrr with 60451 elements. Creating vector time with 60451 elements. Creating vector cal_striing with 60451 elements. Creating vector time with 60451 elements. Creating vector avg_biolume with 60451 elements. Creating vector time with 60451 elements. Creating vector pump with 60451 elements. Creating vector time with 60451 elements. Creating vector system_voltage with 60451 elements. Creating vector time with 60451 elements. Creating vector flow with 60451 elements. Creating vector time with 60451 elements. Creating vector HV with 60451 elements. Creating vector time with 60451 elements. Creating vector reserved with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_0 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_1 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_2 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_3 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_4 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_5 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_6 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_7 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_8 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_9 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_10 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_11 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_12 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_13 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_14 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_15 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_16 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_17 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_18 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_19 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_20 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_21 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_22 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_23 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_24 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_25 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_26 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_27 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_28 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_29 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_30 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_31 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_32 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_33 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_34 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_35 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_36 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_37 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_38 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_39 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_40 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_41 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_42 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_43 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_44 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_45 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_46 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_47 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_48 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_49 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_50 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_51 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_52 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_53 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_54 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_55 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_56 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_57 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_58 with 60451 elements. Creating vector time with 60451 elements. Creating vector raw_59 with 60451 elements. Creating vector time with 60451 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/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/2011/2011111/2011.111.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (3682 x 994) with 3659908 elements. Creating vector time with 3682 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (3682 x 994) with 3659908 elements. Creating vector time with 3682 elements. Creating vector bin with 994 elements. Creating matrix countList (3682 x 994) with 3659908 elements. Creating vector time with 3682 elements. Creating vector bin with 994 elements. Creating vector LCcount with 3682 elements. Creating vector time with 3682 elements. Creating vector transCount with 3682 elements. Creating vector time with 3682 elements. Creating vector nonTransCount with 3682 elements. Creating vector time with 3682 elements. Creating vector ai_mean with 3682 elements. Creating vector time with 3682 elements. Creating vector ai_min with 3682 elements. Creating vector time with 3682 elements. Creating vector ai_max with 3682 elements. Creating vector time with 3682 elements. Creating vector ai_std with 3682 elements. Creating vector time with 3682 elements. Creating vector esd_mean with 3682 elements. Creating vector time with 3682 elements. Creating vector esd_min with 3682 elements. Creating vector time with 3682 elements. Creating vector esd_max with 3682 elements. Creating vector time with 3682 elements. Creating vector esd_std with 3682 elements. Creating vector time with 3682 elements. Creating vector countSum with 3682 elements. Creating vector time with 3682 elements. Creating vector snapshot with 3682 elements. Creating vector time with 3682 elements. Creating vector threshold with 3682 elements. Creating vector time with 3682 elements. Creating vector sampleCount with 3682 elements. Creating vector time with 3682 elements. Creating vector flowCount with 3682 elements. Creating vector time with 3682 elements. Creating vector flowTime with 3682 elements. Creating vector time with 3682 elements. Creating vector bufferStatus with 3682 elements. Creating vector time with 3682 elements. Creating vector laserLevel with 3682 elements. Creating vector time with 3682 elements. Creating vector counter with 3682 elements. Creating vector time with 3682 elements. Creating vector counterPeriod with 3682 elements. Creating vector time with 3682 elements. Creating vector laserControl with 3682 elements. Creating vector time with 3682 elements. Creating vector countUnknownFrameCharacter with 3682 elements. Creating vector time with 3682 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 3682 elements. Creating vector time with 3682 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 3682 elements. Creating vector time with 3682 elements. Creating vector flowSpeed with 3682 elements. Creating vector time with 3682 elements. Creating vector countShortLFrameError with 3682 elements. Creating vector time with 3682 elements. Creating vector countGarbledLFrame with 3682 elements. Creating vector time with 3682 elements. Creating vector cFrameEsecs with 3682 elements. Creating vector time with 3682 elements. Creating vector correctedSampleCountList with 3682 elements. Creating vector time with 3682 elements. Creating vector time with 3682 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011111/2011.111.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011.111.00.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_2011.111.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 27 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_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 = 356 Gridding with nix = 1068, iZ = 78 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 [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 355) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] transCount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 357) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] nonTransCount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 359) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] LCcount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 361) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 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 299136 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 299136 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 118878 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 04/21/2011 12:30 to 04/22/2011 07:29 swr = NaN 988.8148 899.9294 747.4645 512.1086 307.8608 116.9873 36.7851 NaN NaN 2.1253 1.4233 1.9367 1.2000 1.5368 1.6366 1.7267 1.5333 11.7967 158.4770 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2011111_GulperTimes.txt && touch ../results/2011111_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/2011/2011111/2011.111.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2011/2011111/2011.111.00/syslog -startEsecs 1303421337.8558 -surveyName Dorado389_2011_111_00_111_00 >> ../results/2011111_GulperTimes.txt Executing: removeGulpDups.py ../results/2011111_GulperTimes.txt Bottle: 0 Time: 1303425446 Depth: 5.2559 Dist: 4.1981 Bottle: 1 Time: 1303427315 Depth: 5.5366 Dist: 6.1739 Bottle: 2 Time: 1303429250 Depth: 5.4557 Dist: 8.4265 Bottle: 3 Time: 1303438249 Depth: 4.3189 Dist: 16.1178 Bottle: 4 Time: 1303439908 Depth: 5.3504 Dist: 18.1312 Bottle: 5 Time: 1303441893 Depth: 5.6174 Dist: 20.2786 Bottle: 6 Time: 1303461078 Depth: 5.4638 Dist: 36.8745 Bottle: 7 Time: 1303463298 Depth: 5.6045 Dist: 39.2461 Bottle: 8 Time: 1303465288 Depth: 5.4442 Dist: 41.4716 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_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 2Column contouring gridded variable gT 2Column contouring gridded variable gS 2Column contouring gridded variable gN 2Column contouring gridded variable gO 2Column contouring gridded variable gB420 2Column contouring gridded variable gB700 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_2column.png Elapsed time to save image: 9 seconds Biolume contouring gridded variable gD Biolume contouring gridded variable gT Biolume contouring gridded variable gS Biolume contouring gridded variable gN Biolume contouring gridded variable gO Biolume contouring gridded variable gB420 Biolume contouring gridded variable gB700 Biolume contouring gridded variable gF Biolume contouring gridded variable gBL Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_biolume.png Elapsed time to save image: 39 seconds 2Column contouring gridded variable gLOPCcount 2Column contouring gridded variable gLOPCtransCount 2Column contouring gridded variable gLOPCnonTransCount 2Column contouring gridded variable gLOPCLCcount 2Column contouring gridded variable gT 2Column contouring gridded variable gB420 2Column contouring gridded variable gB700 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_lopc.png Elapsed time to save image: 7 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_2column.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2011/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2011/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2011/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2011/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2011/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2011/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2011/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2011/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath); Could not do interp1: The grid vectors must contain unique points. Did not write KML for this variable. Rethrowing error. Could not create .kmz for LOPC Total Count Creating Dorado389_2011_111_00_111_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00.kml... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_111_00_111_00_Bioluminescence.kml' not found.] [> In create_data_products (line 414) In build_auv_survey (line 522) In AUVprocess_main (line 255)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Encountered 1257 NaN values in array of lon that is 47702 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 46445 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 46445 are not equal to number of Lat lon points = 47702 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_2011_111_00_111_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00.txt... Copied to /mbari/AUVCTD/surveys/2011/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2011/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... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2011/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_2011_111_00_111_00.nc... Copied to /mbari/AUVCTD/surveys/2011/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2011/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_111_00_111_00.mat... Copied to /mbari/AUVCTD/surveys/2011/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2011_111_00_111_00 processed" mccann@mbari.org < mail_Dorado389_2011_111_00_111_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011.111.00.mat Processing time: 335 seconds