Execution of AUVprocess_main version 1.86 at 2018-05-30T19:57:29Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2006, ['138.01'], '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: 2006.138.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/ 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/2006/2006138/2006.138.01/navigation.nc') Creating vector time with 307201 elements. Creating vector mPos_x with 307201 elements. Creating vector time with 307201 elements. Creating vector mPos_y with 307201 elements. Creating vector time with 307201 elements. Creating vector mDepth with 307201 elements. Creating vector time with 307201 elements. Creating vector mGpsNorth with 307201 elements. Creating vector time with 307201 elements. Creating vector mGpsEast with 307201 elements. Creating vector time with 307201 elements. Creating vector mGpsValid with 307201 elements. Creating vector time with 307201 elements. Creating vector mPhi with 307201 elements. Creating vector time with 307201 elements. Creating vector mTheta with 307201 elements. Creating vector time with 307201 elements. Creating vector mPsi with 307201 elements. Creating vector time with 307201 elements. Creating vector mOmega_x with 307201 elements. Creating vector time with 307201 elements. Creating vector mOmega_y with 307201 elements. Creating vector time with 307201 elements. Creating vector mOmega_z with 307201 elements. Creating vector time with 307201 elements. Creating vector mPsaRange with 307201 elements. Creating vector time with 307201 elements. Creating vector mAltitude with 307201 elements. Creating vector time with 307201 elements. Creating vector mDvlAltitude with 307201 elements. Creating vector time with 307201 elements. Creating vector mWaterSpeed with 307201 elements. Creating vector time with 307201 elements. Creating vector mDvlValid with 307201 elements. Creating vector time with 307201 elements. Creating vector mDvlNewData with 307201 elements. Creating vector time with 307201 elements. Creating vector mDeltaT with 307201 elements. Creating vector time with 307201 elements. Creating vector nfix with 307201 elements. Creating vector time with 307201 elements. Creating vector efix with 307201 elements. Creating vector time with 307201 elements. Creating vector filter_north with 307201 elements. Creating vector time with 307201 elements. Creating vector filter_east with 307201 elements. Creating vector time with 307201 elements. Creating vector filter_depth with 307201 elements. Creating vector time with 307201 elements. Creating vector north_current with 307201 elements. Creating vector time with 307201 elements. Creating vector east_current with 307201 elements. Creating vector time with 307201 elements. Creating vector speed_bias with 307201 elements. Creating vector time with 307201 elements. Creating vector heading_bias with 307201 elements. Creating vector time with 307201 elements. Creating vector latitude with 307201 elements. Creating vector time with 307201 elements. Creating vector longitude with 307201 elements. Creating vector time with 307201 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/navigation.nc'); processNav(): median of positive valued depths = 130.6348 processNav(): Finding depths less than 914.4436 and times > 0 processNav(): length(Nav.depth) = 307201 processNav(): length(gindx) = 307201 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/2006/2006138/2006.138.01/gps.nc') Creating vector time with 1855 elements. Creating vector hours with 1855 elements. Creating vector time with 1855 elements. Creating vector minutes with 1855 elements. Creating vector time with 1855 elements. Creating vector seconds with 1855 elements. Creating vector time with 1855 elements. Creating vector centiSeconds with 1855 elements. Creating vector time with 1855 elements. Creating vector latitude with 1855 elements. Creating vector time with 1855 elements. Creating vector longitude with 1855 elements. Creating vector time with 1855 elements. Creating vector quality with 1855 elements. Creating vector time with 1855 elements. Creating vector numberOfSatellites with 1855 elements. Creating vector time with 1855 elements. Creating vector hdop with 1855 elements. Creating vector time with 1855 elements. Creating vector antennaHeight with 1855 elements. Creating vector time with 1855 elements. Creating vector geoHeight with 1855 elements. Creating vector time with 1855 elements. Creating vector dgpsDataAge with 1855 elements. Creating vector time with 1855 elements. Creating vector dgpsRSID with 1855 elements. Creating vector time with 1855 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/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/2006/2006138/2006.138.01/parosci.nc') Creating vector time with 659023 elements. Creating vector depth with 659023 elements. Creating vector time with 659023 elements. Creating vector temp with 659023 elements. Creating vector time with 659023 elements. Creating vector pressure with 659023 elements. Creating vector time with 659023 elements. Creating vector temp_period with 659023 elements. Creating vector time with 659023 elements. Creating vector pres_period with 659023 elements. Creating vector time with 659023 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.39488 max(Depth.data) = 290.2529 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.39488 max(Depth.data) = 290.2529 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/2006/2006138/2006.138.01/hydroscatlog.nc') Creating vector time with 245736 elements. Creating vector Seconds with 245736 elements. Creating vector time with 245736 elements. Creating vector HundrethsOfSeconds with 245736 elements. Creating vector time with 245736 elements. Creating vector Snorm1 with 245736 elements. Creating vector time with 245736 elements. Creating vector Snorm2 with 245736 elements. Creating vector time with 245736 elements. Creating vector Snorm3 with 245736 elements. Creating vector time with 245736 elements. Creating vector Gain_Status_1 with 245736 elements. Creating vector time with 245736 elements. Creating vector Gain_Status_2 with 245736 elements. Creating vector time with 245736 elements. Creating vector Gain_Status_3 with 245736 elements. Creating vector time with 245736 elements. Creating vector RawDepthValue with 245736 elements. Creating vector time with 245736 elements. Creating vector RawTempValue with 245736 elements. Creating vector time with 245736 elements. Creating vector Temperature with 245736 elements. Creating vector time with 245736 elements. Creating vector ErrorValue with 245736 elements. Creating vector time with 245736 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/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/2006/2006138/2006.138.01/ctdDriver.nc') Creating vector time with 245782 elements. Creating vector conductivity with 245782 elements. Creating vector time with 245782 elements. Creating vector temperature with 245782 elements. Creating vector time with 245782 elements. Creating vector cond_frequency with 245782 elements. Creating vector time with 245782 elements. Creating vector temp_frequency with 245782 elements. Creating vector time with 245782 elements. Creating vector spare with 245782 elements. Creating vector time with 245782 elements. Creating vector humidity with 245782 elements. Creating vector time with 245782 elements. Creating vector flow1 with 245782 elements. Creating vector time with 245782 elements. Creating vector OBS with 245782 elements. Creating vector time with 245782 elements. Creating vector dissolvedO2 with 245782 elements. Creating vector time with 245782 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/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/2006/2006138/2006.138.01/ctdDriver2.nc') Creating vector time with 245776 elements. Creating vector conductivity with 245776 elements. Creating vector time with 245776 elements. Creating vector temperature with 245776 elements. Creating vector time with 245776 elements. Creating vector cond_frequency with 245776 elements. Creating vector time with 245776 elements. Creating vector temp_frequency with 245776 elements. Creating vector time with 245776 elements. Creating vector flow2 with 245776 elements. Creating vector time with 245776 elements. Creating vector spare with 245776 elements. Creating vector time with 245776 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/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/2006/2006138/2006.138.01/isuslog.nc') Creating vector time with 41583 elements. Creating vector isusNitrate with 41583 elements. Creating vector time with 41583 elements. Creating vector isusTemp with 41583 elements. Creating vector time with 41583 elements. Creating vector isusQuality with 41583 elements. Creating vector time with 41583 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/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/2006/2006138/2006.138.01/biolume.nc') Creating vector time with 61474 elements. Creating vector rrr with 61474 elements. Creating vector time with 61474 elements. Creating vector cal_striing with 61474 elements. Creating vector time with 61474 elements. Creating vector pump with 61474 elements. Creating vector time with 61474 elements. Creating vector flow with 61474 elements. Creating vector time with 61474 elements. Creating vector humidity with 61474 elements. Creating vector time with 61474 elements. Creating vector temperature with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_0 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_1 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_2 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_3 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_4 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_5 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_6 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_7 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_8 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_9 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_10 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_11 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_12 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_13 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_14 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_15 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_16 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_17 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_18 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_19 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_20 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_21 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_22 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_23 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_24 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_25 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_26 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_27 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_28 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_29 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_30 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_31 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_32 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_33 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_34 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_35 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_36 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_37 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_38 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_39 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_40 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_41 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_42 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_43 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_44 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_45 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_46 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_47 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_48 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_49 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_50 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_51 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_52 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_53 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_54 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_55 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_56 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_57 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_58 with 61474 elements. Creating vector time with 61474 elements. Creating vector raw_59 with 61474 elements. Creating vector time with 61474 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006138/2006.138.01/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/2006/2006138/2006.138.01/lopc.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/2006/2006138/2006.138.01/lopc.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/2006/2006138/2006.138.01/lopc.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/2006/2006138/2006.138.01/lopc.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 lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006.138.01.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_2006.138.01.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_2006_138_01_138_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_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 = 120 Gridding with nix = 360, iZ = 581 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... bbp470 [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 231) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] bbp676 [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 253) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] fl676_uncorr [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 274) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] N [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 304) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] BL BLflow LOPC Only one good point or fewer - NaNing the gLOPCcount array. - NaNing the gLOPCtransCount array. - NaNing the gLOPCnonTransCount array. - NaNing the gLOPCLCcount array. Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB470 cvarname = gB676 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount No valid data for gLOPCcount cvarname = gLOPCtransCount No valid data for gLOPCtransCount cvarname = gLOPCnonTransCount No valid data for gLOPCnonTransCount cvarname = gLOPCLCcount No valid data for gLOPCLCcount Encountered 0 NaN values in array of lon that is 305906 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: Some input points were outside the grid domain(s). grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447) No depth array returned by grdtrack. Perhaps grdtrack could not be found in the search path. Setting ocean depths to 4000m for the track. Getting short wave radiation data from M1 for little plot above the biolume section plot Creating vector TIME with 119041 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 05/18/2006 09:30 to 05/19/2006 04:29 swr = 180.0491 245.5208 335.5461 483.3398 446.8260 472.7140 312.5646 230.4735 122.1874 52.3025 8.7253 0.7232 NaN NaN NaN NaN NaN NaN NaN NaN Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2006138_GulperTimes.txt && touch ../results/2006138_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/2006/2006138/2006.138.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2006/2006138/2006.138.01/syslog -startEsecs 1147977696.362 -surveyName Dorado389_2006_138_01_138_01 >> ../results/2006138_GulperTimes.txt Executing: removeGulpDups.py ../results/2006138_GulperTimes.txt Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_gridded.mat outvarstr = 'gF gT gN gS gD gO gB470 gB676 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 gB470 2Column contouring gridded variable gB676 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_2006_138_01_138_01_2column.png Elapsed time to save image: 11 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 gB470 Biolume contouring gridded variable gB676 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_2006_138_01_138_01_biolume.png Elapsed time to save image: 53 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 gB470 2Column contouring gridded variable gB676 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_2006_138_01_138_01_lopc.png Elapsed time to save image: 11 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_2006_138_01_138_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_2column.png... Copied to /mbari/AUVCTD/surveys/2006/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_biolume.png... Copied to /mbari/AUVCTD/surveys/2006/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_lopc.png... Copied to /mbari/AUVCTD/surveys/2006/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2006/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2006/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2006/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_2006_138_01_138_01_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_138_01_138_01_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2006/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_2006_138_01_138_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_138_01_138_01_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2006/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); 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 Nitrate 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_2006_138_01_138_01_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_138_01_138_01_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2006/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @470 nm', jetplus, varlimits(5,:), hs2.bbp470, time.hs2, auvnav, depth.hs2, 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 Optical Backscatter @470 nm KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, 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 Optical Backscatter @676 nm KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, 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 Chlorophyll Fluorescence 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_2006_138_01_138_01_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_138_01_138_01_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2006/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); length(v_esecs(gindx)) = which is less than 2. Not processing. adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_138_01_138_01_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_138_01_138_01_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2006/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2006_138_01_138_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01.kml... Copied to /mbari/AUVCTD/surveys/2006/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_138_01_138_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_2006_138_01_138_01.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 13 NaNs found in bbpRed. Interpolating anyway. Encountered 175 NaN values in array of lon that is 41575 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: Some input points were outside the grid domain(s). grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447) No depth array returned by grdtrack. Setting bottom depth to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01.txt... Copied to /mbari/AUVCTD/surveys/2006/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_Gulper.txt... Tried, but failed to copy to /mbari/AUVCTD/surveys/2006/odv/ cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_Gulper.txt’: No such file or directory ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 13 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_decim.nc... Copied to /mbari/AUVCTD/surveys/2006/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_2006_138_01_138_01.nc... Copied to /mbari/AUVCTD/surveys/2006/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01_gridded.mat... Copied to /mbari/AUVCTD/surveys/2006/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_138_01_138_01.mat... Copied to /mbari/AUVCTD/surveys/2006/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2006_138_01_138_01 processed" mccann@mbari.org < mail_Dorado389_2006_138_01_138_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006.138.01.mat Processing time: 225 seconds