Execution of AUVprocess_main version 1.86 at 2018-05-30T18:42:05Z on elvis Matlab command executed: AUVprocess_main('BIOLUME', 2006, ['054.00'], '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: 2006.054.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/ 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/2006/2006054/2006.054.00/navigation.nc') Creating vector time with 109454 elements. Creating vector mPos_x with 109454 elements. Creating vector time with 109454 elements. Creating vector mPos_y with 109454 elements. Creating vector time with 109454 elements. Creating vector mDepth with 109454 elements. Creating vector time with 109454 elements. Creating vector mGpsNorth with 109454 elements. Creating vector time with 109454 elements. Creating vector mGpsEast with 109454 elements. Creating vector time with 109454 elements. Creating vector mGpsValid with 109454 elements. Creating vector time with 109454 elements. Creating vector mPhi with 109454 elements. Creating vector time with 109454 elements. Creating vector mTheta with 109454 elements. Creating vector time with 109454 elements. Creating vector mPsi with 109454 elements. Creating vector time with 109454 elements. Creating vector mOmega_x with 109454 elements. Creating vector time with 109454 elements. Creating vector mOmega_y with 109454 elements. Creating vector time with 109454 elements. Creating vector mOmega_z with 109454 elements. Creating vector time with 109454 elements. Creating vector mPsaRange with 109454 elements. Creating vector time with 109454 elements. Creating vector mAltitude with 109454 elements. Creating vector time with 109454 elements. Creating vector mDvlAltitude with 109454 elements. Creating vector time with 109454 elements. Creating vector mWaterSpeed with 109454 elements. Creating vector time with 109454 elements. Creating vector mDvlValid with 109454 elements. Creating vector time with 109454 elements. Creating vector mDvlNewData with 109454 elements. Creating vector time with 109454 elements. Creating vector mDeltaT with 109454 elements. Creating vector time with 109454 elements. Creating vector nfix with 109454 elements. Creating vector time with 109454 elements. Creating vector efix with 109454 elements. Creating vector time with 109454 elements. Creating vector filter_north with 109454 elements. Creating vector time with 109454 elements. Creating vector filter_east with 109454 elements. Creating vector time with 109454 elements. Creating vector filter_depth with 109454 elements. Creating vector time with 109454 elements. Creating vector north_current with 109454 elements. Creating vector time with 109454 elements. Creating vector east_current with 109454 elements. Creating vector time with 109454 elements. Creating vector speed_bias with 109454 elements. Creating vector time with 109454 elements. Creating vector heading_bias with 109454 elements. Creating vector time with 109454 elements. Creating vector latitude with 109454 elements. Creating vector time with 109454 elements. Creating vector longitude with 109454 elements. Creating vector time with 109454 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/navigation.nc'); processNav(): median of positive valued depths = 32.3298 processNav(): Finding depths less than 226.3088 and times > 0 processNav(): length(Nav.depth) = 109454 processNav(): length(gindx) = 109454 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/2006/2006054/2006.054.00/gps.nc') Creating vector time with 4279 elements. Creating vector hours with 4279 elements. Creating vector time with 4279 elements. Creating vector minutes with 4279 elements. Creating vector time with 4279 elements. Creating vector seconds with 4279 elements. Creating vector time with 4279 elements. Creating vector centiSeconds with 4279 elements. Creating vector time with 4279 elements. Creating vector latitude with 4279 elements. Creating vector time with 4279 elements. Creating vector longitude with 4279 elements. Creating vector time with 4279 elements. Creating vector quality with 4279 elements. Creating vector time with 4279 elements. Creating vector numberOfSatellites with 4279 elements. Creating vector time with 4279 elements. Creating vector hdop with 4279 elements. Creating vector time with 4279 elements. Creating vector antennaHeight with 4279 elements. Creating vector time with 4279 elements. Creating vector geoHeight with 4279 elements. Creating vector time with 4279 elements. Creating vector dgpsDataAge with 4279 elements. Creating vector time with 4279 elements. Creating vector dgpsRSID with 4279 elements. Creating vector time with 4279 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/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/2006/2006054/2006.054.00/parosci.nc') Creating vector time with 234341 elements. Creating vector depth with 234341 elements. Creating vector time with 234341 elements. Creating vector temp with 234341 elements. Creating vector time with 234341 elements. Creating vector pressure with 234341 elements. Creating vector time with 234341 elements. Creating vector temp_period with 234341 elements. Creating vector time with 234341 elements. Creating vector pres_period with 234341 elements. Creating vector time with 234341 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -1.177 max(Depth.data) = 341.4947 Found 2483 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.99995 max(Depth.data) = 293.4687 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/2006/2006054/2006.054.00/hydroscatlog.nc') Creating vector time with 87591 elements. Creating vector Seconds with 87591 elements. Creating vector time with 87591 elements. Creating vector HundrethsOfSeconds with 87591 elements. Creating vector time with 87591 elements. Creating vector Snorm1 with 87591 elements. Creating vector time with 87591 elements. Creating vector Snorm2 with 87591 elements. Creating vector time with 87591 elements. Creating vector Snorm3 with 87591 elements. Creating vector time with 87591 elements. Creating vector Gain_Status_1 with 87591 elements. Creating vector time with 87591 elements. Creating vector Gain_Status_2 with 87591 elements. Creating vector time with 87591 elements. Creating vector Gain_Status_3 with 87591 elements. Creating vector time with 87591 elements. Creating vector RawDepthValue with 87591 elements. Creating vector time with 87591 elements. Creating vector RawTempValue with 87591 elements. Creating vector time with 87591 elements. Creating vector Temperature with 87591 elements. Creating vector time with 87591 elements. Creating vector ErrorValue with 87591 elements. Creating vector time with 87591 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/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/2006/2006054/2006.054.00/ctdDriver.nc') Creating vector time with 87544 elements. Creating vector conductivity with 87544 elements. Creating vector time with 87544 elements. Creating vector temperature with 87544 elements. Creating vector time with 87544 elements. Creating vector cond_frequency with 87544 elements. Creating vector time with 87544 elements. Creating vector temp_frequency with 87544 elements. Creating vector time with 87544 elements. Creating vector spare with 87544 elements. Creating vector time with 87544 elements. Creating vector humidity with 87544 elements. Creating vector time with 87544 elements. Creating vector flow1 with 87544 elements. Creating vector time with 87544 elements. Creating vector OBS with 87544 elements. Creating vector time with 87544 elements. Creating vector dissolvedO2 with 87544 elements. Creating vector time with 87544 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/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/2006/2006054/2006.054.00/ctdDriver2.nc') Creating vector time with 87544 elements. Creating vector conductivity with 87544 elements. Creating vector time with 87544 elements. Creating vector temperature with 87544 elements. Creating vector time with 87544 elements. Creating vector cond_frequency with 87544 elements. Creating vector time with 87544 elements. Creating vector temp_frequency with 87544 elements. Creating vector time with 87544 elements. Creating vector flow2 with 87544 elements. Creating vector time with 87544 elements. Creating vector spare with 87544 elements. Creating vector time with 87544 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/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/2006/2006054/2006.054.00/isuslog.nc') Creating vector time with 1401 elements. Creating vector isusNitrate with 1401 elements. Creating vector time with 1401 elements. Creating vector isusTemp with 1401 elements. Creating vector time with 1401 elements. Creating vector isusQuality with 1401 elements. Creating vector time with 1401 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/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/2006/2006054/2006.054.00/biolume.nc') Creating vector time with 21915 elements. Creating vector rrr with 21915 elements. Creating vector time with 21915 elements. Creating vector cal_striing with 21915 elements. Creating vector time with 21915 elements. Creating vector pump with 21915 elements. Creating vector time with 21915 elements. Creating vector flow with 21915 elements. Creating vector time with 21915 elements. Creating vector humidity with 21915 elements. Creating vector time with 21915 elements. Creating vector temperature with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_0 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_1 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_2 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_3 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_4 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_5 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_6 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_7 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_8 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_9 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_10 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_11 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_12 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_13 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_14 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_15 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_16 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_17 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_18 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_19 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_20 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_21 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_22 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_23 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_24 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_25 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_26 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_27 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_28 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_29 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_30 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_31 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_32 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_33 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_34 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_35 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_36 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_37 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_38 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_39 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_40 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_41 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_42 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_43 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_44 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_45 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_46 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_47 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_48 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_49 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_50 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_51 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_52 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_53 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_54 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_55 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_56 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_57 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_58 with 21915 elements. Creating vector time with 21915 elements. Creating vector raw_59 with 21915 elements. Creating vector time with 21915 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006054/2006.054.00/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/2006/2006054/2006.054.00/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/2006/2006054/2006.054.00/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/2006/2006054/2006.054.00/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/2006/2006054/2006.054.00/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_2006.054.00.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_2006.054.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 8 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_054_00_054_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_054_00_054_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_054_00_054_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 = 166 Gridding with nix = 498, iZ = 243 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 bbp676 fl676_uncorr N 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 92283 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 92283 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 119040 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 02/22/2006 16:30 to 02/23/2006 00:29 swr = 199.6876 35.7657 0.6000 NaN NaN NaN NaN NaN NaN Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_054_00_054_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2006054_GulperTimes.txt && touch ../results/2006054_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/2006/2006054/2006.054.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2006/2006054/2006.054.00/syslog -startEsecs 1140660907.6379 -surveyName Dorado389_2006_054_00_054_00 >> ../results/2006054_GulperTimes.txt Executing: removeGulpDups.py ../results/2006054_GulperTimes.txt Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_054_00_054_00_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 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 gB470 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB676 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_2006_054_00_054_00_2column.png Elapsed time to save image: 10 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 gB470 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB676 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_2006_054_00_054_00_biolume.png Elapsed time to save image: 35 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 gB470 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB676 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_2006_054_00_054_00_lopc.png Elapsed time to save image: 10 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_054_00_054_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_054_00_054_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_054_00_054_00_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_054_00_054_00_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_054_00_054_00_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_054_00_054_00_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_054_00_054_00_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_054_00_054_00_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_054_00_054_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_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_054_00_054_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_Nitrate.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, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_Optical_Backscatter_470_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_Optical_Backscatter_470_nm.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 @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_Optical_Backscatter_676_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_Optical_Backscatter_676_nm.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, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_Chlorophyll_Fluorescence.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, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_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_054_00_054_00_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_054_00_054_00_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_054_00_054_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_054_00_054_00.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_054_00_054_00_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_054_00_054_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1045 NaNs found in bbpBlue. Interpolating anyway. 1036 NaNs found in bbpRed. Interpolating anyway. Encountered 222 NaN values in array of lon that is 1401 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 1179 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 1179 are not equal to number of Lat lon points = 1401 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_2006_054_00_054_00.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_054_00_054_00.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_054_00_054_00_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_054_00_054_00_Gulper.txt’: No such file or directory ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1045 NaNs found in bbpBlue. Interpolating anyway. 1036 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_054_00_054_00_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_054_00_054_00.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_054_00_054_00_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_054_00_054_00.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_054_00_054_00 processed" mccann@mbari.org < mail_Dorado389_2006_054_00_054_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006.054.00.mat Processing time: 125 seconds