Execution of AUVprocess_main version 1.86 at 2018-05-29T21:49:58Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2008, ['140.00'], '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: 2008.140.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/ 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/2008/2008140/2008.140.00/navigation.nc') Creating vector time with 374792 elements. Creating vector mPos_x with 374792 elements. Creating vector time with 374792 elements. Creating vector mPos_y with 374792 elements. Creating vector time with 374792 elements. Creating vector mDepth with 374792 elements. Creating vector time with 374792 elements. Creating vector mGpsNorth with 374792 elements. Creating vector time with 374792 elements. Creating vector mGpsEast with 374792 elements. Creating vector time with 374792 elements. Creating vector mGpsValid with 374792 elements. Creating vector time with 374792 elements. Creating vector mPhi with 374792 elements. Creating vector time with 374792 elements. Creating vector mTheta with 374792 elements. Creating vector time with 374792 elements. Creating vector mPsi with 374792 elements. Creating vector time with 374792 elements. Creating vector mOmega_x with 374792 elements. Creating vector time with 374792 elements. Creating vector mOmega_y with 374792 elements. Creating vector time with 374792 elements. Creating vector mOmega_z with 374792 elements. Creating vector time with 374792 elements. Creating vector mPsaRange with 374792 elements. Creating vector time with 374792 elements. Creating vector mAltitude with 374792 elements. Creating vector time with 374792 elements. Creating vector mDvlAltitude with 374792 elements. Creating vector time with 374792 elements. Creating vector mWaterSpeed with 374792 elements. Creating vector time with 374792 elements. Creating vector mDvlValid with 374792 elements. Creating vector time with 374792 elements. Creating vector mDvlNewData with 374792 elements. Creating vector time with 374792 elements. Creating vector mDeltaT with 374792 elements. Creating vector time with 374792 elements. Creating vector nfix with 374792 elements. Creating vector time with 374792 elements. Creating vector efix with 374792 elements. Creating vector time with 374792 elements. Creating vector filter_north with 374792 elements. Creating vector time with 374792 elements. Creating vector filter_east with 374792 elements. Creating vector time with 374792 elements. Creating vector filter_depth with 374792 elements. Creating vector time with 374792 elements. Creating vector north_current with 374792 elements. Creating vector time with 374792 elements. Creating vector east_current with 374792 elements. Creating vector time with 374792 elements. Creating vector speed_bias with 374792 elements. Creating vector time with 374792 elements. Creating vector heading_bias with 374792 elements. Creating vector time with 374792 elements. Creating vector latitude with 374792 elements. Creating vector time with 374792 elements. Creating vector longitude with 374792 elements. Creating vector time with 374792 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/navigation.nc'); processNav(): median of positive valued depths = 10.6526 processNav(): Finding depths less than 74.5683 and times > 0 processNav(): length(Nav.depth) = 374792 processNav(): length(gindx) = 374792 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/2008/2008140/2008.140.00/gps.nc') Creating vector time with 3357 elements. Creating vector hours with 3357 elements. Creating vector time with 3357 elements. Creating vector minutes with 3357 elements. Creating vector time with 3357 elements. Creating vector seconds with 3357 elements. Creating vector time with 3357 elements. Creating vector centiSeconds with 3357 elements. Creating vector time with 3357 elements. Creating vector latitude with 3357 elements. Creating vector time with 3357 elements. Creating vector longitude with 3357 elements. Creating vector time with 3357 elements. Creating vector quality with 3357 elements. Creating vector time with 3357 elements. Creating vector numberOfSatellites with 3357 elements. Creating vector time with 3357 elements. Creating vector hdop with 3357 elements. Creating vector time with 3357 elements. Creating vector antennaHeight with 3357 elements. Creating vector time with 3357 elements. Creating vector geoHeight with 3357 elements. Creating vector time with 3357 elements. Creating vector dgpsDataAge with 3357 elements. Creating vector time with 3357 elements. Creating vector dgpsRSID with 3357 elements. Creating vector time with 3357 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/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/2008/2008140/2008.140.00/parosci.nc') Creating vector time with 647499 elements. Creating vector depth with 647499 elements. Creating vector time with 647499 elements. Creating vector temp with 647499 elements. Creating vector time with 647499 elements. Creating vector pressure with 647499 elements. Creating vector time with 647499 elements. Creating vector temp_period with 647499 elements. Creating vector time with 647499 elements. Creating vector pres_period with 647499 elements. Creating vector time with 647499 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.80663 max(Depth.data) = 21.8759 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.80663 max(Depth.data) = 21.8759 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/2008/2008140/2008.140.00/hydroscatlog.nc') Creating vector time with 299789 elements. Creating vector Seconds with 299789 elements. Creating vector time with 299789 elements. Creating vector HundrethsOfSeconds with 299789 elements. Creating vector time with 299789 elements. Creating vector Snorm1 with 299789 elements. Creating vector time with 299789 elements. Creating vector Snorm2 with 299789 elements. Creating vector time with 299789 elements. Creating vector Snorm3 with 299789 elements. Creating vector time with 299789 elements. Creating vector Gain_Status_1 with 299789 elements. Creating vector time with 299789 elements. Creating vector Gain_Status_2 with 299789 elements. Creating vector time with 299789 elements. Creating vector Gain_Status_3 with 299789 elements. Creating vector time with 299789 elements. Creating vector RawDepthValue with 299789 elements. Creating vector time with 299789 elements. Creating vector RawTempValue with 299789 elements. Creating vector time with 299789 elements. Creating vector Temperature with 299789 elements. Creating vector time with 299789 elements. Creating vector ErrorValue with 299789 elements. Creating vector time with 299789 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/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/2008/2008140/2008.140.00/ctdDriver.nc') Creating vector time with 299610 elements. Creating vector conductivity with 299610 elements. Creating vector time with 299610 elements. Creating vector temperature with 299610 elements. Creating vector time with 299610 elements. Creating vector cond_frequency with 299610 elements. Creating vector time with 299610 elements. Creating vector temp_frequency with 299610 elements. Creating vector time with 299610 elements. Creating vector spare with 299610 elements. Creating vector time with 299610 elements. Creating vector humidity with 299610 elements. Creating vector time with 299610 elements. Creating vector flow1 with 299610 elements. Creating vector time with 299610 elements. Creating vector CDOM with 299610 elements. Creating vector time with 299610 elements. Creating vector dissolvedO2 with 299610 elements. Creating vector time with 299610 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/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/2008/2008140/2008.140.00/ctdDriver2.nc') Creating vector time with 299715 elements. Creating vector conductivity with 299715 elements. Creating vector time with 299715 elements. Creating vector temperature with 299715 elements. Creating vector time with 299715 elements. Creating vector cond_frequency with 299715 elements. Creating vector time with 299715 elements. Creating vector temp_frequency with 299715 elements. Creating vector time with 299715 elements. Creating vector flow2 with 299715 elements. Creating vector time with 299715 elements. Creating vector spare with 299715 elements. Creating vector time with 299715 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/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/2008/2008140/2008.140.00/isuslog.nc') Creating vector time with 58287 elements. Creating vector isusNitrate with 58287 elements. Creating vector time with 58287 elements. Creating vector isusTemp with 58287 elements. Creating vector time with 58287 elements. Creating vector isusQuality with 58287 elements. Creating vector time with 58287 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/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/2008/2008140/2008.140.00/biolume.nc') Creating vector time with 75000 elements. Creating vector rrr with 75000 elements. Creating vector time with 75000 elements. Creating vector cal_striing with 75000 elements. Creating vector time with 75000 elements. Creating vector pump with 75000 elements. Creating vector time with 75000 elements. Creating vector flow with 75000 elements. Creating vector time with 75000 elements. Creating vector humidity with 75000 elements. Creating vector time with 75000 elements. Creating vector temperature with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_0 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_1 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_2 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_3 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_4 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_5 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_6 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_7 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_8 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_9 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_10 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_11 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_12 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_13 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_14 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_15 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_16 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_17 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_18 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_19 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_20 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_21 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_22 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_23 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_24 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_25 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_26 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_27 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_28 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_29 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_30 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_31 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_32 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_33 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_34 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_35 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_36 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_37 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_38 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_39 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_40 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_41 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_42 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_43 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_44 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_45 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_46 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_47 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_48 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_49 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_50 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_51 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_52 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_53 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_54 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_55 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_56 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_57 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_58 with 75000 elements. Creating vector time with 75000 elements. Creating vector raw_59 with 75000 elements. Creating vector time with 75000 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/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/2008/2008140/2008.140.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (2620 x 994) with 2604280 elements. Creating vector time with 2620 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (2620 x 994) with 2604280 elements. Creating vector time with 2620 elements. Creating vector bin with 994 elements. Creating matrix countList (2620 x 994) with 2604280 elements. Creating vector time with 2620 elements. Creating vector bin with 994 elements. Creating vector LCcount with 2620 elements. Creating vector time with 2620 elements. Creating vector transCount with 2620 elements. Creating vector time with 2620 elements. Creating vector nonTransCount with 2620 elements. Creating vector time with 2620 elements. Creating vector ai_mean with 2620 elements. Creating vector time with 2620 elements. Creating vector ai_min with 2620 elements. Creating vector time with 2620 elements. Creating vector ai_max with 2620 elements. Creating vector time with 2620 elements. Creating vector ai_std with 2620 elements. Creating vector time with 2620 elements. Creating vector esd_mean with 2620 elements. Creating vector time with 2620 elements. Creating vector esd_min with 2620 elements. Creating vector time with 2620 elements. Creating vector esd_max with 2620 elements. Creating vector time with 2620 elements. Creating vector esd_std with 2620 elements. Creating vector time with 2620 elements. Creating vector countSum with 2620 elements. Creating vector time with 2620 elements. Creating vector snapshot with 2620 elements. Creating vector time with 2620 elements. Creating vector threshold with 2620 elements. Creating vector time with 2620 elements. Creating vector sampleCount with 2620 elements. Creating vector time with 2620 elements. Creating vector flowCount with 2620 elements. Creating vector time with 2620 elements. Creating vector flowTime with 2620 elements. Creating vector time with 2620 elements. Creating vector bufferStatus with 2620 elements. Creating vector time with 2620 elements. Creating vector laserLevel with 2620 elements. Creating vector time with 2620 elements. Creating vector counter with 2620 elements. Creating vector time with 2620 elements. Creating vector counterPeriod with 2620 elements. Creating vector time with 2620 elements. Creating vector laserControl with 2620 elements. Creating vector time with 2620 elements. Creating vector countUnknownFrameCharacter with 2620 elements. Creating vector time with 2620 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 2620 elements. Creating vector time with 2620 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 2620 elements. Creating vector time with 2620 elements. Creating vector flowSpeed with 2620 elements. Creating vector time with 2620 elements. Creating vector countShortLFrameError with 2620 elements. Creating vector time with 2620 elements. Creating vector countGarbledLFrame with 2620 elements. Creating vector time with 2620 elements. Creating vector correctedSampleCountList with 2620 elements. Creating vector time with 2620 elements. Creating vector time with 2620 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008140/2008.140.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008.140.00.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_2008.140.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 30 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_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 = 1608 Gridding with nix = 4824, iZ = 41 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 373579 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 373579 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 119019 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 05/19/2008 12:30 to 05/20/2008 11:30 swr = 651.1221 563.9972 417.4495 302.3400 266.0000 128.9000 70.9800 18.4400 4.4800 4.2400 4.1800 4.2400 4.1800 4.1262 4.1107 3.9492 4.1351 4.0600 13.3600 46.2200 124.8200 176.5394 287.1717 397.7707 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2008140_GulperTimes.txt && touch ../results/2008140_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/2008/2008140/2008.140.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2008/2008140/2008.140.00/syslog -startEsecs 1211232289.0914 -surveyName Dorado389_2008_140_00_140_00 >> ../results/2008140_GulperTimes.txt Executing: removeGulpDups.py ../results/2008140_GulperTimes.txt Bottle: 0 Time: 1211294162.2928 Depth: 10.6478 Dist: 80.1053 Bottle: 1 Time: 1211294164.4927 Depth: 11.3017 Dist: 80.1075 Bottle: 2 Time: 1211296637.0933 Depth: 10.7881 Dist: 83.1074 Bottle: 3 Time: 1211296639.2931 Depth: 11.5922 Dist: 83.1103 Bottle: 4 Time: 1211300721.0935 Depth: 10.1864 Dist: 88.4089 Bottle: 5 Time: 1211300723.2933 Depth: 11.3392 Dist: 88.4108 Bottle: 6 Time: 1211304897.0874 Depth: 10.553 Dist: 93.7506 Bottle: 7 Time: 1211304899.2873 Depth: 10.9208 Dist: 93.7528 Bottle 8 time is 96.6434 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Bottle 9 time is 98.8432 seconds greater than nearest time in (sub)section auvnav.fixTime vector. Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_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 2Column contouring gridded variable gT 2Column contouring gridded variable gS 2Column contouring gridded variable gN 2Column contouring gridded variable gO 2Column contouring gridded variable gB470 2Column contouring gridded variable gB676 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_2column.png Elapsed time to save image: 13 seconds Biolume contouring gridded variable gD Biolume contouring gridded variable gT Biolume contouring gridded variable gS Biolume contouring gridded variable gN Biolume contouring gridded variable gO Biolume contouring gridded variable gB470 Biolume contouring gridded variable gB676 Biolume contouring gridded variable gF Biolume contouring gridded variable gBL Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_biolume.png Elapsed time to save image: 69 seconds 2Column contouring gridded variable gLOPCcount 2Column contouring gridded variable gLOPCtransCount 2Column contouring gridded variable gLOPCnonTransCount 2Column contouring gridded variable gLOPCLCcount 2Column contouring gridded variable gT 2Column contouring gridded variable gB470 2Column contouring gridded variable gB676 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_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_2008_140_00_140_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_2column.png... Copied to /mbari/AUVCTD/surveys/2008/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2008/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2008/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2008/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2008/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2008/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_2008_140_00_140_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_140_00_140_00_Temperature.kmz... Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/ cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory 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_2008_140_00_140_00_Salinity.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_140_00_140_00_Salinity.kmz... Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/ cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory 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_2008_140_00_140_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_140_00_140_00_Nitrate.kmz... Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/ cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory 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_2008_140_00_140_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_140_00_140_00_Oxygen.kmz... Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/ cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory 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_2008_140_00_140_00_Optical_Backscatter_470_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_140_00_140_00_Optical_Backscatter_470_nm.kmz... Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/ cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory 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_2008_140_00_140_00_Optical_Backscatter_676_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_140_00_140_00_Optical_Backscatter_676_nm.kmz... Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/ cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory 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_2008_140_00_140_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_140_00_140_00_Chlorophyll_Fluorescence.kmz... Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/ cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory 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_2008_140_00_140_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_140_00_140_00_Bioluminescence.kmz... Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/ cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory 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_2008_140_00_140_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00.kml... Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/ cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 26 NaNs found in bbpBlue. Interpolating anyway. 17 NaNs found in bbpRed. Interpolating anyway. Encountered 191 NaN values in array of lon that is 58287 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 58096 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 58096 are not equal to number of Lat lon points = 58287 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_2008_140_00_140_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00.txt... Copied to /mbari/AUVCTD/surveys/2008/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2008/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... 26 NaNs found in bbpBlue. Interpolating anyway. 17 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2008/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_2008_140_00_140_00.nc... Copied to /mbari/AUVCTD/surveys/2008/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2008/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_140_00_140_00.mat... Copied to /mbari/AUVCTD/surveys/2008/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2008_140_00_140_00 processed" mccann@mbari.org < mail_Dorado389_2008_140_00_140_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008.140.00.mat Processing time: 410 seconds