Execution of AUVprocess_main version 1.86 at 2018-05-24T21:00:03Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2013, ['298.01'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2013.298.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/navigation.nc') Creating vector time with 68576 elements. Creating vector mPos_x with 68576 elements. Creating vector time with 68576 elements. Creating vector mPos_y with 68576 elements. Creating vector time with 68576 elements. Creating vector mDepth with 68576 elements. Creating vector time with 68576 elements. Creating vector mGpsNorth with 68576 elements. Creating vector time with 68576 elements. Creating vector mGpsEast with 68576 elements. Creating vector time with 68576 elements. Creating vector mGpsValid with 68576 elements. Creating vector time with 68576 elements. Creating vector mPhi with 68576 elements. Creating vector time with 68576 elements. Creating vector mTheta with 68576 elements. Creating vector time with 68576 elements. Creating vector mPsi with 68576 elements. Creating vector time with 68576 elements. Creating vector mOmega_x with 68576 elements. Creating vector time with 68576 elements. Creating vector mOmega_y with 68576 elements. Creating vector time with 68576 elements. Creating vector mOmega_z with 68576 elements. Creating vector time with 68576 elements. Creating vector mPsaRange with 68576 elements. Creating vector time with 68576 elements. Creating vector mAltitude with 68576 elements. Creating vector time with 68576 elements. Creating vector mDvlAltitude with 68576 elements. Creating vector time with 68576 elements. Creating vector mEchoAltitude with 68576 elements. Creating vector time with 68576 elements. Creating vector mEchoHorizRange with 68576 elements. Creating vector time with 68576 elements. Creating vector mEchoAltitudeLast with 68576 elements. Creating vector time with 68576 elements. Creating vector mEchoHorizRangeLast with 68576 elements. Creating vector time with 68576 elements. Creating vector mEchoNumOfPings with 68576 elements. Creating vector time with 68576 elements. Creating vector mWaterSpeed with 68576 elements. Creating vector time with 68576 elements. Creating vector mDvlValid with 68576 elements. Creating vector time with 68576 elements. Creating vector mDvlNewData with 68576 elements. Creating vector time with 68576 elements. Creating vector mDeltaT with 68576 elements. Creating vector time with 68576 elements. Creating vector nfix with 68576 elements. Creating vector time with 68576 elements. Creating vector efix with 68576 elements. Creating vector time with 68576 elements. Creating vector filter_north with 68576 elements. Creating vector time with 68576 elements. Creating vector filter_east with 68576 elements. Creating vector time with 68576 elements. Creating vector filter_depth with 68576 elements. Creating vector time with 68576 elements. Creating vector north_current with 68576 elements. Creating vector time with 68576 elements. Creating vector east_current with 68576 elements. Creating vector time with 68576 elements. Creating vector speed_bias with 68576 elements. Creating vector time with 68576 elements. Creating vector heading_bias with 68576 elements. Creating vector time with 68576 elements. Creating vector latitude with 68576 elements. Creating vector time with 68576 elements. Creating vector longitude with 68576 elements. Creating vector time with 68576 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/navigation.nc'); processNav(): median of positive valued depths = 19.1208 processNav(): Finding depths less than 133.8458 and times > 0 processNav(): length(Nav.depth) = 68576 processNav(): length(gindx) = 68576 Processing GPS navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/gps.nc') Creating vector time with 873 elements. Creating vector hours with 873 elements. Creating vector time with 873 elements. Creating vector minutes with 873 elements. Creating vector time with 873 elements. Creating vector seconds with 873 elements. Creating vector time with 873 elements. Creating vector centiSeconds with 873 elements. Creating vector time with 873 elements. Creating vector latitude with 873 elements. Creating vector time with 873 elements. Creating vector longitude with 873 elements. Creating vector time with 873 elements. Creating vector quality with 873 elements. Creating vector time with 873 elements. Creating vector numberOfSatellites with 873 elements. Creating vector time with 873 elements. Creating vector hdop with 873 elements. Creating vector time with 873 elements. Creating vector antennaHeight with 873 elements. Creating vector time with 873 elements. Creating vector geoHeight with 873 elements. Creating vector time with 873 elements. Creating vector dgpsDataAge with 873 elements. Creating vector time with 873 elements. Creating vector dgpsRSID with 873 elements. Creating vector time with 873 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/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/2013/2013298/2013.298.01/parosci.nc') Creating vector time with 135051 elements. Creating vector depth with 135051 elements. Creating vector time with 135051 elements. Creating vector temp with 135051 elements. Creating vector time with 135051 elements. Creating vector pressure with 135051 elements. Creating vector time with 135051 elements. Creating vector temp_period with 135051 elements. Creating vector time with 135051 elements. Creating vector pres_period with 135051 elements. Creating vector time with 135051 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.27967 max(Depth.data) = 80.3604 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.27967 max(Depth.data) = 80.3604 Processing hs2 backscattering and chlorophyll fluorescence data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/hydroscatlog.nc') Creating vector time with 54942 elements. Creating vector Seconds with 54942 elements. Creating vector time with 54942 elements. Creating vector HundrethsOfSeconds with 54942 elements. Creating vector time with 54942 elements. Creating vector Snorm1 with 54942 elements. Creating vector time with 54942 elements. Creating vector Snorm2 with 54942 elements. Creating vector time with 54942 elements. Creating vector Snorm3 with 54942 elements. Creating vector time with 54942 elements. Creating vector Gain_Status_1 with 54942 elements. Creating vector time with 54942 elements. Creating vector Gain_Status_2 with 54942 elements. Creating vector time with 54942 elements. Creating vector Gain_Status_3 with 54942 elements. Creating vector time with 54942 elements. Creating vector RawDepthValue with 54942 elements. Creating vector time with 54942 elements. Creating vector RawTempValue with 54942 elements. Creating vector time with 54942 elements. Creating vector Temperature with 54942 elements. Creating vector time with 54942 elements. Creating vector ErrorValue with 54942 elements. Creating vector time with 54942 elements. Creating vector bb470 with 54942 elements. Creating vector time with 54942 elements. Creating vector bb676 with 54942 elements. Creating vector time with 54942 elements. Creating vector fl676u with 54942 elements. Creating vector time with 54942 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/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/2013/2013298/2013.298.01/ctdDriver.nc') Creating vector time with 54896 elements. Creating vector conductivity with 54896 elements. Creating vector time with 54896 elements. Creating vector temperature with 54896 elements. Creating vector time with 54896 elements. Creating vector cond_frequency with 54896 elements. Creating vector time with 54896 elements. Creating vector temp_frequency with 54896 elements. Creating vector time with 54896 elements. Creating vector spare with 54896 elements. Creating vector time with 54896 elements. Creating vector humidity with 54896 elements. Creating vector time with 54896 elements. Creating vector flow1 with 54896 elements. Creating vector time with 54896 elements. Creating vector CDOM with 54896 elements. Creating vector time with 54896 elements. Creating vector dissolvedO2 with 54896 elements. Creating vector time with 54896 elements. Creating vector salinity with 54896 elements. Creating vector time with 54896 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/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/2013/2013298/2013.298.01/ctdDriver2.nc') Creating vector time with 54896 elements. Creating vector conductivity with 54896 elements. Creating vector time with 54896 elements. Creating vector temperature with 54896 elements. Creating vector time with 54896 elements. Creating vector cond_frequency with 54896 elements. Creating vector time with 54896 elements. Creating vector temp_frequency with 54896 elements. Creating vector time with 54896 elements. Creating vector flow2 with 54896 elements. Creating vector time with 54896 elements. Creating vector spare with 54896 elements. Creating vector time with 54896 elements. Creating vector salinity with 54896 elements. Creating vector time with 54896 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/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/2013/2013298/2013.298.01/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/2013/2013298/2013.298.01/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/2013/2013298/2013.298.01/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/2013/2013298/2013.298.01/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 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/biolume.nc') Creating vector time with 13521 elements. Creating vector rrr with 13521 elements. Creating vector time with 13521 elements. Creating vector cal_striing with 13521 elements. Creating vector time with 13521 elements. Creating vector avg_biolume with 13521 elements. Creating vector time with 13521 elements. Creating vector pump with 13521 elements. Creating vector time with 13521 elements. Creating vector system_voltage with 13521 elements. Creating vector time with 13521 elements. Creating vector flow with 13521 elements. Creating vector time with 13521 elements. Creating vector HV with 13521 elements. Creating vector time with 13521 elements. Creating vector reserved with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_0 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_1 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_2 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_3 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_4 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_5 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_6 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_7 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_8 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_9 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_10 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_11 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_12 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_13 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_14 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_15 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_16 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_17 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_18 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_19 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_20 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_21 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_22 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_23 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_24 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_25 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_26 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_27 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_28 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_29 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_30 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_31 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_32 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_33 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_34 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_35 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_36 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_37 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_38 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_39 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_40 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_41 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_42 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_43 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_44 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_45 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_46 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_47 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_48 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_49 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_50 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_51 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_52 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_53 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_54 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_55 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_56 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_57 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_58 with 13521 elements. Creating vector time with 13521 elements. Creating vector raw_59 with 13521 elements. Creating vector time with 13521 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/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/2013/2013298/2013.298.01/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (1121 x 994) with 1114274 elements. Creating vector time with 1121 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (1121 x 994) with 1114274 elements. Creating vector time with 1121 elements. Creating vector bin with 994 elements. Creating matrix countList (1121 x 994) with 1114274 elements. Creating vector time with 1121 elements. Creating vector bin with 994 elements. Creating vector LCcount with 1121 elements. Creating vector time with 1121 elements. Creating vector transCount with 1121 elements. Creating vector time with 1121 elements. Creating vector nonTransCount with 1121 elements. Creating vector time with 1121 elements. Creating vector ai_mean with 1121 elements. Creating vector time with 1121 elements. Creating vector ai_min with 1121 elements. Creating vector time with 1121 elements. Creating vector ai_max with 1121 elements. Creating vector time with 1121 elements. Creating vector ai_std with 1121 elements. Creating vector time with 1121 elements. Creating vector esd_mean with 1121 elements. Creating vector time with 1121 elements. Creating vector esd_min with 1121 elements. Creating vector time with 1121 elements. Creating vector esd_max with 1121 elements. Creating vector time with 1121 elements. Creating vector esd_std with 1121 elements. Creating vector time with 1121 elements. Creating vector countSum with 1121 elements. Creating vector time with 1121 elements. Creating vector snapshot with 1121 elements. Creating vector time with 1121 elements. Creating vector threshold with 1121 elements. Creating vector time with 1121 elements. Creating vector sampleCount with 1121 elements. Creating vector time with 1121 elements. Creating vector flowCount with 1121 elements. Creating vector time with 1121 elements. Creating vector flowTime with 1121 elements. Creating vector time with 1121 elements. Creating vector bufferStatus with 1121 elements. Creating vector time with 1121 elements. Creating vector laserLevel with 1121 elements. Creating vector time with 1121 elements. Creating vector counter with 1121 elements. Creating vector time with 1121 elements. Creating vector counterPeriod with 1121 elements. Creating vector time with 1121 elements. Creating vector laserControl with 1121 elements. Creating vector time with 1121 elements. Creating vector countUnknownFrameCharacter with 1121 elements. Creating vector time with 1121 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 1121 elements. Creating vector time with 1121 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 1121 elements. Creating vector time with 1121 elements. Creating vector flowSpeed with 1121 elements. Creating vector time with 1121 elements. Creating vector countShortLFrameError with 1121 elements. Creating vector time with 1121 elements. Creating vector countGarbledLFrame with 1121 elements. Creating vector time with 1121 elements. Creating vector cFrameEsecs with 1121 elements. Creating vector time with 1121 elements. Creating vector correctedSampleCountList with 1121 elements. Creating vector time with 1121 elements. Creating vector time with 1121 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.298.01.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/src/matlab/doradosdp/results/Dorado389_2013.298.01.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 9 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_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 = 114 Gridding with nix = 342, iZ = 158 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 63597 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 63597 points from grid Monterey25.grd (2876 x 2447) Getting short wave radiation data from M1 for little plot above the biolume section plot Creating vector TIME with 118898 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 10/25/2013 10:29 to 10/25/2013 16:29 swr = 362.0534 564.6931 598.0508 537.0553 528.1254 394.7917 231.0552 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_swr.png [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 564) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Done plotting SWR. Executing: /bin/rm -f ../results/2013298_GulperTimes.txt && touch ../results/2013298_GulperTimes.txt Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013298/2013.298.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013298/2013.298.01/syslog -startEsecs 1382728378.9326 -surveyName Dorado389_2013_298_01_298_01 >> ../results/2013298_GulperTimes.txt Executing: removeGulpDups.py ../results/2013298_GulperTimes.txt Bottle: 0 Time: 1382735462 Depth: 10.6123 Dist: 8.3921 Bottle: 1 Time: 1382736255 Depth: 13.0477 Dist: 9.411 Bottle: 2 Time: 1382737081 Depth: 8.5521 Dist: 10.5396 Bottle: 3 Time: 1382737855 Depth: 15.9845 Dist: 11.5679 Bottle: 4 Time: 1382738309 Depth: 12.6248 Dist: 12.1797 Bottle: 5 Time: 1382739004 Depth: 7.3021 Dist: 13.1069 Bottle: 6 Time: 1382739509 Depth: 5.9995 Dist: 13.7935 Bottle: 7 Time: 1382739970 Depth: 3.0685 Dist: 14.4111 Bottle: 8 Time: 1382741075 Depth: 3.2303 Dist: 15.8942 Bottle 9 time is 380.8687 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_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/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_2column.png Elapsed time to save image: 9 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN Drawing bottom contour from EM300 data Biolume contouring gridded variable gO Drawing bottom contour from EM300 data Biolume contouring gridded variable gB420 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB700 Drawing bottom contour from EM300 data Biolume contouring gridded variable gF Drawing bottom contour from EM300 data Biolume contouring gridded variable gBL Drawing bottom contour from EM300 data Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_biolume.png Elapsed time to save image: 33 seconds 2Column contouring gridded variable gLOPCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCtransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCnonTransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCLCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_lopc.png Elapsed time to save image: 9 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_2column.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_biolume.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_lopc.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing KML files ... KML = write_kml(survey_shrt_filename_base, 'Temperature', jetplus, varlimits(1,:), ctd1.T, time.ctd1, auvnav, depth.ctd1, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath); length(v_esecs(gindx)) = which is less than 2. Not processing. updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @420 nm', jetplus, varlimits(5,:), hs2.bbp420, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Optical_Backscatter_420_nm.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @700 nm', jetplus, varlimits(6,:), hs2.bbp700, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Chlorophyll_Fluorescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_LOPC_Total_Count.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2013_298_01_298_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01.kml... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_298_01_298_01_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 414) In build_auv_survey (line 522) In AUVprocess_main (line 255)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01.mat ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Encountered 0 NaN values in array of lon that is 5490 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 5490 points from grid Monterey25.grd (2876 x 2447) Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01.txt... Copied to /mbari/AUVCTD/surveys/2013/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2013/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_decim.nc... Copied to /mbari/AUVCTD/surveys/2013/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01.nc... Copied to /mbari/AUVCTD/surveys/2013/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01_gridded.mat... Copied to /mbari/AUVCTD/surveys/2013/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_298_01_298_01.mat... Copied to /mbari/AUVCTD/surveys/2013/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2013_298_01_298_01 processed" mccann@mbari.org < mail_Dorado389_2013_298_01_298_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.298.01.mat Processing time: 103 seconds