Execution of AUVprocess_main version 1.86 at 2018-05-30T17:37:02Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2007, ['344.00'], '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: 2007.344.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/ 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/2007/2007344/2007.344.00/navigation.nc') Creating vector time with 356287 elements. Creating vector mPos_x with 356287 elements. Creating vector time with 356287 elements. Creating vector mPos_y with 356287 elements. Creating vector time with 356287 elements. Creating vector mDepth with 356287 elements. Creating vector time with 356287 elements. Creating vector mGpsNorth with 356287 elements. Creating vector time with 356287 elements. Creating vector mGpsEast with 356287 elements. Creating vector time with 356287 elements. Creating vector mGpsValid with 356287 elements. Creating vector time with 356287 elements. Creating vector mPhi with 356287 elements. Creating vector time with 356287 elements. Creating vector mTheta with 356287 elements. Creating vector time with 356287 elements. Creating vector mPsi with 356287 elements. Creating vector time with 356287 elements. Creating vector mOmega_x with 356287 elements. Creating vector time with 356287 elements. Creating vector mOmega_y with 356287 elements. Creating vector time with 356287 elements. Creating vector mOmega_z with 356287 elements. Creating vector time with 356287 elements. Creating vector mPsaRange with 356287 elements. Creating vector time with 356287 elements. Creating vector mAltitude with 356287 elements. Creating vector time with 356287 elements. Creating vector mDvlAltitude with 356287 elements. Creating vector time with 356287 elements. Creating vector mWaterSpeed with 356287 elements. Creating vector time with 356287 elements. Creating vector mDvlValid with 356287 elements. Creating vector time with 356287 elements. Creating vector mDvlNewData with 356287 elements. Creating vector time with 356287 elements. Creating vector mDeltaT with 356287 elements. Creating vector time with 356287 elements. Creating vector nfix with 356287 elements. Creating vector time with 356287 elements. Creating vector efix with 356287 elements. Creating vector time with 356287 elements. Creating vector filter_north with 356287 elements. Creating vector time with 356287 elements. Creating vector filter_east with 356287 elements. Creating vector time with 356287 elements. Creating vector filter_depth with 356287 elements. Creating vector time with 356287 elements. Creating vector north_current with 356287 elements. Creating vector time with 356287 elements. Creating vector east_current with 356287 elements. Creating vector time with 356287 elements. Creating vector speed_bias with 356287 elements. Creating vector time with 356287 elements. Creating vector heading_bias with 356287 elements. Creating vector time with 356287 elements. Creating vector latitude with 356287 elements. Creating vector time with 356287 elements. Creating vector longitude with 356287 elements. Creating vector time with 356287 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/navigation.nc'); processNav(): median of positive valued depths = 76.9447 processNav(): Finding depths less than 538.6127 and times > 0 processNav(): length(Nav.depth) = 356287 processNav(): length(gindx) = 356287 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/2007/2007344/2007.344.00/gps.nc') Creating vector time with 1716 elements. Creating vector hours with 1716 elements. Creating vector time with 1716 elements. Creating vector minutes with 1716 elements. Creating vector time with 1716 elements. Creating vector seconds with 1716 elements. Creating vector time with 1716 elements. Creating vector centiSeconds with 1716 elements. Creating vector time with 1716 elements. Creating vector latitude with 1716 elements. Creating vector time with 1716 elements. Creating vector longitude with 1716 elements. Creating vector time with 1716 elements. Creating vector quality with 1716 elements. Creating vector time with 1716 elements. Creating vector numberOfSatellites with 1716 elements. Creating vector time with 1716 elements. Creating vector hdop with 1716 elements. Creating vector time with 1716 elements. Creating vector antennaHeight with 1716 elements. Creating vector time with 1716 elements. Creating vector geoHeight with 1716 elements. Creating vector time with 1716 elements. Creating vector dgpsDataAge with 1716 elements. Creating vector time with 1716 elements. Creating vector dgpsRSID with 1716 elements. Creating vector time with 1716 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/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/2007/2007344/2007.344.00/parosci.nc') Creating vector time with 625598 elements. Creating vector depth with 625598 elements. Creating vector time with 625598 elements. Creating vector temp with 625598 elements. Creating vector time with 625598 elements. Creating vector pressure with 625598 elements. Creating vector time with 625598 elements. Creating vector temp_period with 625598 elements. Creating vector time with 625598 elements. Creating vector pres_period with 625598 elements. Creating vector time with 625598 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.61939 max(Depth.data) = 250.903 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.61939 max(Depth.data) = 250.903 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/2007/2007344/2007.344.00/hydroscatlog.nc') Creating vector time with 285000 elements. Creating vector Seconds with 285000 elements. Creating vector time with 285000 elements. Creating vector HundrethsOfSeconds with 285000 elements. Creating vector time with 285000 elements. Creating vector Snorm1 with 285000 elements. Creating vector time with 285000 elements. Creating vector Snorm2 with 285000 elements. Creating vector time with 285000 elements. Creating vector Snorm3 with 285000 elements. Creating vector time with 285000 elements. Creating vector Gain_Status_1 with 285000 elements. Creating vector time with 285000 elements. Creating vector Gain_Status_2 with 285000 elements. Creating vector time with 285000 elements. Creating vector Gain_Status_3 with 285000 elements. Creating vector time with 285000 elements. Creating vector RawDepthValue with 285000 elements. Creating vector time with 285000 elements. Creating vector RawTempValue with 285000 elements. Creating vector time with 285000 elements. Creating vector Temperature with 285000 elements. Creating vector time with 285000 elements. Creating vector ErrorValue with 285000 elements. Creating vector time with 285000 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/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/2007/2007344/2007.344.00/ctdDriver.nc') Creating vector time with 284975 elements. Creating vector conductivity with 284975 elements. Creating vector time with 284975 elements. Creating vector temperature with 284975 elements. Creating vector time with 284975 elements. Creating vector cond_frequency with 284975 elements. Creating vector time with 284975 elements. Creating vector temp_frequency with 284975 elements. Creating vector time with 284975 elements. Creating vector spare with 284975 elements. Creating vector time with 284975 elements. Creating vector humidity with 284975 elements. Creating vector time with 284975 elements. Creating vector flow1 with 284975 elements. Creating vector time with 284975 elements. Creating vector CDOM with 284975 elements. Creating vector time with 284975 elements. Creating vector dissolvedO2 with 284975 elements. Creating vector time with 284975 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/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/2007/2007344/2007.344.00/ctdDriver2.nc') Creating vector time with 285042 elements. Creating vector conductivity with 285042 elements. Creating vector time with 285042 elements. Creating vector temperature with 285042 elements. Creating vector time with 285042 elements. Creating vector cond_frequency with 285042 elements. Creating vector time with 285042 elements. Creating vector temp_frequency with 285042 elements. Creating vector time with 285042 elements. Creating vector flow2 with 285042 elements. Creating vector time with 285042 elements. Creating vector spare with 285042 elements. Creating vector time with 285042 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/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/2007/2007344/2007.344.00/isuslog.nc') Creating vector time with 55414 elements. Creating vector isusNitrate with 55414 elements. Creating vector time with 55414 elements. Creating vector isusTemp with 55414 elements. Creating vector time with 55414 elements. Creating vector isusQuality with 55414 elements. Creating vector time with 55414 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/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/2007/2007344/2007.344.00/biolume.nc') Creating vector time with 71299 elements. Creating vector rrr with 71299 elements. Creating vector time with 71299 elements. Creating vector cal_striing with 71299 elements. Creating vector time with 71299 elements. Creating vector pump with 71299 elements. Creating vector time with 71299 elements. Creating vector flow with 71299 elements. Creating vector time with 71299 elements. Creating vector humidity with 71299 elements. Creating vector time with 71299 elements. Creating vector temperature with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_0 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_1 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_2 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_3 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_4 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_5 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_6 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_7 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_8 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_9 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_10 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_11 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_12 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_13 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_14 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_15 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_16 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_17 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_18 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_19 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_20 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_21 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_22 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_23 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_24 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_25 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_26 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_27 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_28 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_29 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_30 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_31 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_32 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_33 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_34 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_35 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_36 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_37 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_38 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_39 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_40 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_41 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_42 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_43 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_44 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_45 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_46 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_47 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_48 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_49 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_50 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_51 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_52 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_53 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_54 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_55 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_56 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_57 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_58 with 71299 elements. Creating vector time with 71299 elements. Creating vector raw_59 with 71299 elements. Creating vector time with 71299 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/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/2007/2007344/2007.344.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (5023 x 994) with 4992862 elements. Creating vector time with 5023 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (5023 x 994) with 4992862 elements. Creating vector time with 5023 elements. Creating vector bin with 994 elements. Creating matrix countList (5023 x 994) with 4992862 elements. Creating vector time with 5023 elements. Creating vector bin with 994 elements. Creating vector LCcount with 5023 elements. Creating vector time with 5023 elements. Creating vector transCount with 5023 elements. Creating vector time with 5023 elements. Creating vector nonTransCount with 5023 elements. Creating vector time with 5023 elements. Creating vector ai_mean with 5023 elements. Creating vector time with 5023 elements. Creating vector ai_min with 5023 elements. Creating vector time with 5023 elements. Creating vector ai_max with 5023 elements. Creating vector time with 5023 elements. Creating vector ai_std with 5023 elements. Creating vector time with 5023 elements. Creating vector esd_mean with 5023 elements. Creating vector time with 5023 elements. Creating vector esd_min with 5023 elements. Creating vector time with 5023 elements. Creating vector esd_max with 5023 elements. Creating vector time with 5023 elements. Creating vector esd_std with 5023 elements. Creating vector time with 5023 elements. Creating vector countSum with 5023 elements. Creating vector time with 5023 elements. Creating vector snapshot with 5023 elements. Creating vector time with 5023 elements. Creating vector threshold with 5023 elements. Creating vector time with 5023 elements. Creating vector sampleCount with 5023 elements. Creating vector time with 5023 elements. Creating vector flowCount with 5023 elements. Creating vector time with 5023 elements. Creating vector flowTime with 5023 elements. Creating vector time with 5023 elements. Creating vector bufferStatus with 5023 elements. Creating vector time with 5023 elements. Creating vector laserLevel with 5023 elements. Creating vector time with 5023 elements. Creating vector counter with 5023 elements. Creating vector time with 5023 elements. Creating vector counterPeriod with 5023 elements. Creating vector time with 5023 elements. Creating vector laserControl with 5023 elements. Creating vector time with 5023 elements. Creating vector countUnknownFrameCharacter with 5023 elements. Creating vector time with 5023 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 5023 elements. Creating vector time with 5023 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 5023 elements. Creating vector time with 5023 elements. Creating vector flowSpeed with 5023 elements. Creating vector time with 5023 elements. Creating vector countShortLFrameError with 5023 elements. Creating vector time with 5023 elements. Creating vector countGarbledLFrame with 5023 elements. Creating vector time with 5023 elements. Creating vector correctedSampleCountList with 5023 elements. Creating vector time with 5023 elements. Creating vector time with 5023 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007344/2007.344.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007.344.00.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_2007.344.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 14 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_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 = 110 Gridding with nix = 330, iZ = 501 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 count [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 355) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] transCount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 357) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] nonTransCount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 359) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] LCcount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 361) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB470 cvarname = gB676 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount cvarname = gLOPCtransCount cvarname = gLOPCnonTransCount cvarname = gLOPCLCcount Encountered 0 NaN values in array of lon that is 356066 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 356066 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 119039 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 12/10/2007 12:29 to 12/11/2007 09:29 swr = NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN 3.1095 2.7566 3.1629 2.8372 3.5578 20.9569 142.4930 226.4482 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2007344_GulperTimes.txt && touch ../results/2007344_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/2007/2007344/2007.344.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2007/2007344/2007.344.00/syslog -startEsecs 1197324696.1647 -surveyName Dorado389_2007_344_00_344_00 >> ../results/2007344_GulperTimes.txt Executing: removeGulpDups.py ../results/2007344_GulperTimes.txt Bottle: 0 Time: 1197324726.9626 Depth: -0.027999 Dist: 0.0064225 Bottle: 1 Time: 1197324729.1624 Depth: -0.1034 Dist: 0.0068814 Bottle: 2 Time: 1197324731.3623 Depth: 0.13255 Dist: 0.0073403 Bottle: 3 Time: 1197324733.5621 Depth: -0.027999 Dist: 0.0077992 Bottle: 4 Time: 1197324735.762 Depth: -0.02082 Dist: 0.0082581 Bottle: 5 Time: 1197324737.9618 Depth: -0.027999 Dist: 0.0092942 Bottle: 6 Time: 1197324740.1617 Depth: -0.027999 Dist: 0.010459 Bottle: 7 Time: 1197324742.3615 Depth: -0.11058 Dist: 0.011623 Bottle: 8 Time: 1197324744.5614 Depth: -0.02082 Dist: 0.012787 Bottle: 9 Time: 1197324746.7612 Depth: -0.02082 Dist: 0.013952 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_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_2007_344_00_344_00_2column.png Elapsed time to save image: 13 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_2007_344_00_344_00_biolume.png Elapsed time to save image: 48 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_2007_344_00_344_00_lopc.png Elapsed time to save image: 15 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_2007_344_00_344_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_2column.png... Copied to /mbari/AUVCTD/surveys/2007/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2007/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2007/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2007/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2007/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2007/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_2007_344_00_344_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_344_00_344_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2007/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_2007_344_00_344_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_344_00_344_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2007/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_2007_344_00_344_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_344_00_344_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2007/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_2007_344_00_344_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_344_00_344_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2007/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_2007_344_00_344_00_Optical_Backscatter_470_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_344_00_344_00_Optical_Backscatter_470_nm.kmz... Copied to /mbari/AUVCTD/surveys/2007/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_2007_344_00_344_00_Optical_Backscatter_676_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_344_00_344_00_Optical_Backscatter_676_nm.kmz... Copied to /mbari/AUVCTD/surveys/2007/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_2007_344_00_344_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_344_00_344_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2007/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_2007_344_00_344_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_344_00_344_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2007/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath); Could not do interp1: The grid vectors must contain unique points. Did not write KML for this variable. Rethrowing error. Could not create .kmz for LOPC Total Count Creating Dorado389_2007_344_00_344_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00.kml... Copied to /mbari/AUVCTD/surveys/2007/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_344_00_344_00_Bioluminescence.kml' not found.] [> In create_data_products (line 414) In build_auv_survey (line 522) In AUVprocess_main (line 255)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 12 NaNs found in bbpRed. Interpolating anyway. Encountered 36 NaN values in array of lon that is 55414 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 55378 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 55378 are not equal to number of Lat lon points = 55414 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_2007_344_00_344_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00.txt... Copied to /mbari/AUVCTD/surveys/2007/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2007/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 12 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2007/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_2007_344_00_344_00.nc... Copied to /mbari/AUVCTD/surveys/2007/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2007/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_344_00_344_00.mat... Copied to /mbari/AUVCTD/surveys/2007/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2007_344_00_344_00 processed" mccann@mbari.org < mail_Dorado389_2007_344_00_344_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007.344.00.mat Processing time: 489 seconds