Execution of AUVprocess_main version 1.86 at 2018-05-29T17:48:29Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2009, ['124.03'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd2') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2009.124.03 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/ 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/2009/2009124/2009.124.03/navigation.nc') Creating vector time with 349738 elements. Creating vector mPos_x with 349738 elements. Creating vector time with 349738 elements. Creating vector mPos_y with 349738 elements. Creating vector time with 349738 elements. Creating vector mDepth with 349738 elements. Creating vector time with 349738 elements. Creating vector mGpsNorth with 349738 elements. Creating vector time with 349738 elements. Creating vector mGpsEast with 349738 elements. Creating vector time with 349738 elements. Creating vector mGpsValid with 349738 elements. Creating vector time with 349738 elements. Creating vector mPhi with 349738 elements. Creating vector time with 349738 elements. Creating vector mTheta with 349738 elements. Creating vector time with 349738 elements. Creating vector mPsi with 349738 elements. Creating vector time with 349738 elements. Creating vector mOmega_x with 349738 elements. Creating vector time with 349738 elements. Creating vector mOmega_y with 349738 elements. Creating vector time with 349738 elements. Creating vector mOmega_z with 349738 elements. Creating vector time with 349738 elements. Creating vector mPsaRange with 349738 elements. Creating vector time with 349738 elements. Creating vector mAltitude with 349738 elements. Creating vector time with 349738 elements. Creating vector mDvlAltitude with 349738 elements. Creating vector time with 349738 elements. Creating vector mWaterSpeed with 349738 elements. Creating vector time with 349738 elements. Creating vector mDvlValid with 349738 elements. Creating vector time with 349738 elements. Creating vector mDvlNewData with 349738 elements. Creating vector time with 349738 elements. Creating vector mDeltaT with 349738 elements. Creating vector time with 349738 elements. Creating vector nfix with 349738 elements. Creating vector time with 349738 elements. Creating vector efix with 349738 elements. Creating vector time with 349738 elements. Creating vector filter_north with 349738 elements. Creating vector time with 349738 elements. Creating vector filter_east with 349738 elements. Creating vector time with 349738 elements. Creating vector filter_depth with 349738 elements. Creating vector time with 349738 elements. Creating vector north_current with 349738 elements. Creating vector time with 349738 elements. Creating vector east_current with 349738 elements. Creating vector time with 349738 elements. Creating vector speed_bias with 349738 elements. Creating vector time with 349738 elements. Creating vector heading_bias with 349738 elements. Creating vector time with 349738 elements. Creating vector latitude with 349738 elements. Creating vector time with 349738 elements. Creating vector longitude with 349738 elements. Creating vector time with 349738 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/navigation.nc'); processNav(): median of positive valued depths = 11.922 processNav(): Finding depths less than 83.4541 and times > 0 processNav(): length(Nav.depth) = 349738 processNav(): length(gindx) = 349738 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/2009/2009124/2009.124.03/gps.nc') Creating vector time with 5660 elements. Creating vector hours with 5660 elements. Creating vector time with 5660 elements. Creating vector minutes with 5660 elements. Creating vector time with 5660 elements. Creating vector seconds with 5660 elements. Creating vector time with 5660 elements. Creating vector centiSeconds with 5660 elements. Creating vector time with 5660 elements. Creating vector latitude with 5660 elements. Creating vector time with 5660 elements. Creating vector longitude with 5660 elements. Creating vector time with 5660 elements. Creating vector quality with 5660 elements. Creating vector time with 5660 elements. Creating vector numberOfSatellites with 5660 elements. Creating vector time with 5660 elements. Creating vector hdop with 5660 elements. Creating vector time with 5660 elements. Creating vector antennaHeight with 5660 elements. Creating vector time with 5660 elements. Creating vector geoHeight with 5660 elements. Creating vector time with 5660 elements. Creating vector dgpsDataAge with 5660 elements. Creating vector time with 5660 elements. Creating vector dgpsRSID with 5660 elements. Creating vector time with 5660 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/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/2009/2009124/2009.124.03/parosci.nc') Creating vector time with 596937 elements. Creating vector depth with 596937 elements. Creating vector time with 596937 elements. Creating vector temp with 596937 elements. Creating vector time with 596937 elements. Creating vector pressure with 596937 elements. Creating vector time with 596937 elements. Creating vector temp_period with 596937 elements. Creating vector time with 596937 elements. Creating vector pres_period with 596937 elements. Creating vector time with 596937 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.54402 max(Depth.data) = 67.2433 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.54402 max(Depth.data) = 67.2433 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/2009/2009124/2009.124.03/hydroscatlog.nc') Creating vector time with 279812 elements. Creating vector Seconds with 279812 elements. Creating vector time with 279812 elements. Creating vector HundrethsOfSeconds with 279812 elements. Creating vector time with 279812 elements. Creating vector Snorm1 with 279812 elements. Creating vector time with 279812 elements. Creating vector Snorm2 with 279812 elements. Creating vector time with 279812 elements. Creating vector Snorm3 with 279812 elements. Creating vector time with 279812 elements. Creating vector Gain_Status_1 with 279812 elements. Creating vector time with 279812 elements. Creating vector Gain_Status_2 with 279812 elements. Creating vector time with 279812 elements. Creating vector Gain_Status_3 with 279812 elements. Creating vector time with 279812 elements. Creating vector RawDepthValue with 279812 elements. Creating vector time with 279812 elements. Creating vector RawTempValue with 279812 elements. Creating vector time with 279812 elements. Creating vector Temperature with 279812 elements. Creating vector time with 279812 elements. Creating vector ErrorValue with 279812 elements. Creating vector time with 279812 elements. Creating vector bb470 with 279812 elements. Creating vector time with 279812 elements. Creating vector bb676 with 279812 elements. Creating vector time with 279812 elements. Creating vector fl676u with 279812 elements. Creating vector time with 279812 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/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/2009/2009124/2009.124.03/ctdDriver.nc') Creating vector time with 279845 elements. Creating vector conductivity with 279845 elements. Creating vector time with 279845 elements. Creating vector temperature with 279845 elements. Creating vector time with 279845 elements. Creating vector cond_frequency with 279845 elements. Creating vector time with 279845 elements. Creating vector temp_frequency with 279845 elements. Creating vector time with 279845 elements. Creating vector spare with 279845 elements. Creating vector time with 279845 elements. Creating vector humidity with 279845 elements. Creating vector time with 279845 elements. Creating vector flow1 with 279845 elements. Creating vector time with 279845 elements. Creating vector CDOM with 279845 elements. Creating vector time with 279845 elements. Creating vector dissolvedO2 with 279845 elements. Creating vector time with 279845 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/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/2009/2009124/2009.124.03/ctdDriver2.nc') Creating vector time with 279862 elements. Creating vector conductivity with 279862 elements. Creating vector time with 279862 elements. Creating vector temperature with 279862 elements. Creating vector time with 279862 elements. Creating vector cond_frequency with 279862 elements. Creating vector time with 279862 elements. Creating vector temp_frequency with 279862 elements. Creating vector time with 279862 elements. Creating vector flow2 with 279862 elements. Creating vector time with 279862 elements. Creating vector spare with 279862 elements. Creating vector time with 279862 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/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/2009/2009124/2009.124.03/isuslog.nc') Creating vector time with 50660 elements. Creating vector isusNitrate with 50660 elements. Creating vector time with 50660 elements. Creating vector isusTemp with 50660 elements. Creating vector time with 50660 elements. Creating vector isusQuality with 50660 elements. Creating vector time with 50660 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/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/2009/2009124/2009.124.03/biolume.nc') Creating vector time with 70015 elements. Creating vector rrr with 70015 elements. Creating vector time with 70015 elements. Creating vector cal_striing with 70015 elements. Creating vector time with 70015 elements. Creating vector pump with 70015 elements. Creating vector time with 70015 elements. Creating vector flow with 70015 elements. Creating vector time with 70015 elements. Creating vector humidity with 70015 elements. Creating vector time with 70015 elements. Creating vector temperature with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_0 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_1 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_2 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_3 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_4 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_5 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_6 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_7 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_8 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_9 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_10 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_11 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_12 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_13 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_14 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_15 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_16 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_17 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_18 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_19 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_20 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_21 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_22 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_23 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_24 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_25 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_26 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_27 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_28 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_29 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_30 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_31 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_32 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_33 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_34 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_35 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_36 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_37 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_38 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_39 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_40 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_41 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_42 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_43 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_44 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_45 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_46 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_47 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_48 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_49 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_50 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_51 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_52 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_53 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_54 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_55 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_56 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_57 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_58 with 70015 elements. Creating vector time with 70015 elements. Creating vector raw_59 with 70015 elements. Creating vector time with 70015 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/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/2009/2009124/2009.124.03/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (4603 x 994) with 4575382 elements. Creating vector time with 4603 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (4603 x 994) with 4575382 elements. Creating vector time with 4603 elements. Creating vector bin with 994 elements. Creating matrix countList (4603 x 994) with 4575382 elements. Creating vector time with 4603 elements. Creating vector bin with 994 elements. Creating vector LCcount with 4603 elements. Creating vector time with 4603 elements. Creating vector transCount with 4603 elements. Creating vector time with 4603 elements. Creating vector nonTransCount with 4603 elements. Creating vector time with 4603 elements. Creating vector ai_mean with 4603 elements. Creating vector time with 4603 elements. Creating vector ai_min with 4603 elements. Creating vector time with 4603 elements. Creating vector ai_max with 4603 elements. Creating vector time with 4603 elements. Creating vector ai_std with 4603 elements. Creating vector time with 4603 elements. Creating vector esd_mean with 4603 elements. Creating vector time with 4603 elements. Creating vector esd_min with 4603 elements. Creating vector time with 4603 elements. Creating vector esd_max with 4603 elements. Creating vector time with 4603 elements. Creating vector esd_std with 4603 elements. Creating vector time with 4603 elements. Creating vector countSum with 4603 elements. Creating vector time with 4603 elements. Creating vector snapshot with 4603 elements. Creating vector time with 4603 elements. Creating vector threshold with 4603 elements. Creating vector time with 4603 elements. Creating vector sampleCount with 4603 elements. Creating vector time with 4603 elements. Creating vector flowCount with 4603 elements. Creating vector time with 4603 elements. Creating vector flowTime with 4603 elements. Creating vector time with 4603 elements. Creating vector bufferStatus with 4603 elements. Creating vector time with 4603 elements. Creating vector laserLevel with 4603 elements. Creating vector time with 4603 elements. Creating vector counter with 4603 elements. Creating vector time with 4603 elements. Creating vector counterPeriod with 4603 elements. Creating vector time with 4603 elements. Creating vector laserControl with 4603 elements. Creating vector time with 4603 elements. Creating vector countUnknownFrameCharacter with 4603 elements. Creating vector time with 4603 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 4603 elements. Creating vector time with 4603 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 4603 elements. Creating vector time with 4603 elements. Creating vector flowSpeed with 4603 elements. Creating vector time with 4603 elements. Creating vector countShortLFrameError with 4603 elements. Creating vector time with 4603 elements. Creating vector countGarbledLFrame with 4603 elements. Creating vector time with 4603 elements. Creating vector correctedSampleCountList with 4603 elements. Creating vector time with 4603 elements. Creating vector time with 4603 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009124/2009.124.03/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009.124.03.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_2009.124.03.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 34 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03.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 = 718 Gridding with nix = 2154, iZ = 103 Using mean boxcar filter of vector... Using mean boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Gridding... T S O Using median boxcar filter of vector... Using median boxcar filter of vector... Using median boxcar filter of vector... bbp420 bbp700 fl700_uncorr N BL BLflow LOPC count [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 355) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] transCount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 357) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] nonTransCount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 359) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] LCcount [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 361) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB420 cvarname = gB700 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount cvarname = gLOPCtransCount cvarname = gLOPCnonTransCount cvarname = gLOPCLCcount Encountered 0 NaN values in array of lon that is 335249 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 335249 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 119015 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 05/04/2009 10:29 to 05/05/2009 07:29 swr = NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_swr.png [Warning: Contour not rendered for non-finite ZData] [> In contourf (line 60) In plot_sections (line 564) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Done plotting SWR. Executing: /bin/rm -f ../results/2009124_GulperTimes.txt && touch ../results/2009124_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/2009/2009124/2009.124.03/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2009/2009124/2009.124.03/syslog -startEsecs 1241463639.7079 -surveyName Dorado389_2009_124_03_124_03 >> ../results/2009124_GulperTimes.txt Executing: removeGulpDups.py ../results/2009124_GulperTimes.txt Bottle: 0 Time: 1241466799 Depth: 6.0568 Dist: 3.9263 Bottle: 1 Time: 1241472943 Depth: 6.1393 Dist: 11.702 Bottle: 2 Time: 1241479475 Depth: 6.0023 Dist: 20.1727 Bottle: 3 Time: 1241488614 Depth: 6.0695 Dist: 30.7998 Bottle: 4 Time: 1241495412.3313 Depth: 6.0265 Dist: 39.3881 Bottle: 5 Time: 1241504429 Depth: 5.5176 Dist: 49.907 Bottle: 6 Time: 1241512115.3371 Depth: 6.0365 Dist: 59.3727 Bottle: 7 Time: 1241515835 Depth: 6.0777 Dist: 64.0651 Bottle: 8 Time: 1241521659 Depth: 6.0623 Dist: 71.3269 Bottle: 9 Time: 1241525381 Depth: 5.8334 Dist: 76.0039 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_gridded.mat outvarstr = 'gF gT gN gS gD gO gB420 gB700 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth ' 2Column contouring gridded variable gD Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gS Drawing bottom contour from EM300 data 2Column contouring gridded variable gN Drawing bottom contour from EM300 data 2Column contouring gridded variable gO Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_2column.png Elapsed time to save image: 12 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN Drawing bottom contour from EM300 data Biolume contouring gridded variable gO Drawing bottom contour from EM300 data Biolume contouring gridded variable gB420 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB700 Drawing bottom contour from EM300 data Biolume contouring gridded variable gF Drawing bottom contour from EM300 data Biolume contouring gridded variable gBL Drawing bottom contour from EM300 data Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_biolume.png Elapsed time to save image: 50 seconds 2Column contouring gridded variable gLOPCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCtransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCnonTransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCLCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_lopc.png Elapsed time to save image: 12 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_2009_124_03_124_03_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_2column.png... Copied to /mbari/AUVCTD/surveys/2009/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_biolume.png... Copied to /mbari/AUVCTD/surveys/2009/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_lopc.png... Copied to /mbari/AUVCTD/surveys/2009/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2009/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2009/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2009/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_2009_124_03_124_03_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2009/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_2009_124_03_124_03_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2009/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_2009_124_03_124_03_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2009/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_2009_124_03_124_03_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2009/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @420 nm', jetplus, varlimits(5,:), hs2.bbp420, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2009/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @700 nm', jetplus, varlimits(6,:), hs2.bbp700, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2009/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2009/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_2009_124_03_124_03_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2009/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_2009_124_03_124_03.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03.kml... Copied to /mbari/AUVCTD/surveys/2009/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_124_03_124_03_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_2009_124_03_124_03.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 10 NaNs found in bbpRed. Interpolating anyway. Encountered 2084 NaN values in array of lon that is 50660 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 48576 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 48576 are not equal to number of Lat lon points = 50660 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_2009_124_03_124_03.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03.txt... Copied to /mbari/AUVCTD/surveys/2009/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2009/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 10 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_decim.nc... Copied to /mbari/AUVCTD/surveys/2009/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_2009_124_03_124_03.nc... Copied to /mbari/AUVCTD/surveys/2009/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03_gridded.mat... Copied to /mbari/AUVCTD/surveys/2009/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_124_03_124_03.mat... Copied to /mbari/AUVCTD/surveys/2009/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2009_124_03_124_03 processed" mccann@mbari.org < mail_Dorado389_2009_124_03_124_03.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009.124.03.mat Processing time: 410 seconds