Execution of AUVprocess_main version 1.86 at 2018-05-23T22:36:53Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2010, ['300.00'], '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: 2010.300.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/ 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/2010/2010300/2010.300.00/navigation.nc') Creating vector time with 323561 elements. Creating vector mPos_x with 323561 elements. Creating vector time with 323561 elements. Creating vector mPos_y with 323561 elements. Creating vector time with 323561 elements. Creating vector mDepth with 323561 elements. Creating vector time with 323561 elements. Creating vector mGpsNorth with 323561 elements. Creating vector time with 323561 elements. Creating vector mGpsEast with 323561 elements. Creating vector time with 323561 elements. Creating vector mGpsValid with 323561 elements. Creating vector time with 323561 elements. Creating vector mPhi with 323561 elements. Creating vector time with 323561 elements. Creating vector mTheta with 323561 elements. Creating vector time with 323561 elements. Creating vector mPsi with 323561 elements. Creating vector time with 323561 elements. Creating vector mOmega_x with 323561 elements. Creating vector time with 323561 elements. Creating vector mOmega_y with 323561 elements. Creating vector time with 323561 elements. Creating vector mOmega_z with 323561 elements. Creating vector time with 323561 elements. Creating vector mPsaRange with 323561 elements. Creating vector time with 323561 elements. Creating vector mAltitude with 323561 elements. Creating vector time with 323561 elements. Creating vector mDvlAltitude with 323561 elements. Creating vector time with 323561 elements. Creating vector mWaterSpeed with 323561 elements. Creating vector time with 323561 elements. Creating vector mDvlValid with 323561 elements. Creating vector time with 323561 elements. Creating vector mDvlNewData with 323561 elements. Creating vector time with 323561 elements. Creating vector mDeltaT with 323561 elements. Creating vector time with 323561 elements. Creating vector nfix with 323561 elements. Creating vector time with 323561 elements. Creating vector efix with 323561 elements. Creating vector time with 323561 elements. Creating vector filter_north with 323561 elements. Creating vector time with 323561 elements. Creating vector filter_east with 323561 elements. Creating vector time with 323561 elements. Creating vector filter_depth with 323561 elements. Creating vector time with 323561 elements. Creating vector north_current with 323561 elements. Creating vector time with 323561 elements. Creating vector east_current with 323561 elements. Creating vector time with 323561 elements. Creating vector speed_bias with 323561 elements. Creating vector time with 323561 elements. Creating vector heading_bias with 323561 elements. Creating vector time with 323561 elements. Creating vector latitude with 323561 elements. Creating vector time with 323561 elements. Creating vector longitude with 323561 elements. Creating vector time with 323561 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/navigation.nc'); processNav(): median of positive valued depths = 15.0542 processNav(): Finding depths less than 105.3793 and times > 0 processNav(): length(Nav.depth) = 323561 processNav(): length(gindx) = 323561 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/2010/2010300/2010.300.00/gps.nc') Creating vector time with 5913 elements. Creating vector hours with 5913 elements. Creating vector time with 5913 elements. Creating vector minutes with 5913 elements. Creating vector time with 5913 elements. Creating vector seconds with 5913 elements. Creating vector time with 5913 elements. Creating vector centiSeconds with 5913 elements. Creating vector time with 5913 elements. Creating vector latitude with 5913 elements. Creating vector time with 5913 elements. Creating vector longitude with 5913 elements. Creating vector time with 5913 elements. Creating vector quality with 5913 elements. Creating vector time with 5913 elements. Creating vector numberOfSatellites with 5913 elements. Creating vector time with 5913 elements. Creating vector hdop with 5913 elements. Creating vector time with 5913 elements. Creating vector antennaHeight with 5913 elements. Creating vector time with 5913 elements. Creating vector geoHeight with 5913 elements. Creating vector time with 5913 elements. Creating vector dgpsDataAge with 5913 elements. Creating vector time with 5913 elements. Creating vector dgpsRSID with 5913 elements. Creating vector time with 5913 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/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/2010/2010300/2010.300.00/parosci.nc') Creating vector time with 592132 elements. Creating vector depth with 592132 elements. Creating vector time with 592132 elements. Creating vector temp with 592132 elements. Creating vector time with 592132 elements. Creating vector pressure with 592132 elements. Creating vector time with 592132 elements. Creating vector temp_period with 592132 elements. Creating vector time with 592132 elements. Creating vector pres_period with 592132 elements. Creating vector time with 592132 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -1.3387 max(Depth.data) = 62.3326 Found 24874 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -1 max(Depth.data) = 62.3326 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/2010/2010300/2010.300.00/hydroscatlog.nc') Creating vector time with 259200 elements. Creating vector Seconds with 259200 elements. Creating vector time with 259200 elements. Creating vector HundrethsOfSeconds with 259200 elements. Creating vector time with 259200 elements. Creating vector Snorm1 with 259200 elements. Creating vector time with 259200 elements. Creating vector Snorm2 with 259200 elements. Creating vector time with 259200 elements. Creating vector Snorm3 with 259200 elements. Creating vector time with 259200 elements. Creating vector Gain_Status_1 with 259200 elements. Creating vector time with 259200 elements. Creating vector Gain_Status_2 with 259200 elements. Creating vector time with 259200 elements. Creating vector Gain_Status_3 with 259200 elements. Creating vector time with 259200 elements. Creating vector RawDepthValue with 259200 elements. Creating vector time with 259200 elements. Creating vector RawTempValue with 259200 elements. Creating vector time with 259200 elements. Creating vector Temperature with 259200 elements. Creating vector time with 259200 elements. Creating vector ErrorValue with 259200 elements. Creating vector time with 259200 elements. Creating vector bb470 with 259200 elements. Creating vector time with 259200 elements. Creating vector bb676 with 259200 elements. Creating vector time with 259200 elements. Creating vector fl676u with 259200 elements. Creating vector time with 259200 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/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/2010/2010300/2010.300.00/ctdDriver.nc') Creating vector time with 259064 elements. Creating vector conductivity with 259064 elements. Creating vector time with 259064 elements. Creating vector temperature with 259064 elements. Creating vector time with 259064 elements. Creating vector cond_frequency with 259064 elements. Creating vector time with 259064 elements. Creating vector temp_frequency with 259064 elements. Creating vector time with 259064 elements. Creating vector spare with 259064 elements. Creating vector time with 259064 elements. Creating vector humidity with 259064 elements. Creating vector time with 259064 elements. Creating vector flow1 with 259064 elements. Creating vector time with 259064 elements. Creating vector rhodamine with 259064 elements. Creating vector time with 259064 elements. Creating vector dissolvedO2 with 259064 elements. Creating vector time with 259064 elements. Creating vector salinity with 259064 elements. Creating vector time with 259064 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/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/2010/2010300/2010.300.00/ctdDriver2.nc') Creating vector time with 259130 elements. Creating vector conductivity with 259130 elements. Creating vector time with 259130 elements. Creating vector temperature with 259130 elements. Creating vector time with 259130 elements. Creating vector cond_frequency with 259130 elements. Creating vector time with 259130 elements. Creating vector temp_frequency with 259130 elements. Creating vector time with 259130 elements. Creating vector flow2 with 259130 elements. Creating vector time with 259130 elements. Creating vector spare with 259130 elements. Creating vector time with 259130 elements. Creating vector salinity with 259130 elements. Creating vector time with 259130 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/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/2010/2010300/2010.300.00/isuslog.nc') Creating vector time with 50372 elements. Creating vector isusNitrate with 50372 elements. Creating vector time with 50372 elements. Creating vector isusTemp with 50372 elements. Creating vector time with 50372 elements. Creating vector isusQuality with 50372 elements. Creating vector time with 50372 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/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/2010/2010300/2010.300.00/biolume.nc') Creating vector time with 63799 elements. Creating vector rrr with 63799 elements. Creating vector time with 63799 elements. Creating vector cal_striing with 63799 elements. Creating vector time with 63799 elements. Creating vector avg_biolume with 63799 elements. Creating vector time with 63799 elements. Creating vector pump with 63799 elements. Creating vector time with 63799 elements. Creating vector system_voltage with 63799 elements. Creating vector time with 63799 elements. Creating vector flow with 63799 elements. Creating vector time with 63799 elements. Creating vector HV with 63799 elements. Creating vector time with 63799 elements. Creating vector reserved with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_0 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_1 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_2 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_3 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_4 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_5 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_6 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_7 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_8 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_9 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_10 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_11 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_12 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_13 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_14 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_15 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_16 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_17 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_18 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_19 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_20 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_21 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_22 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_23 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_24 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_25 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_26 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_27 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_28 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_29 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_30 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_31 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_32 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_33 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_34 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_35 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_36 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_37 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_38 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_39 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_40 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_41 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_42 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_43 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_44 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_45 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_46 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_47 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_48 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_49 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_50 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_51 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_52 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_53 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_54 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_55 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_56 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_57 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_58 with 63799 elements. Creating vector time with 63799 elements. Creating vector raw_59 with 63799 elements. Creating vector time with 63799 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/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/2010/2010300/2010.300.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (6128 x 994) with 6091232 elements. Creating vector time with 6128 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (6128 x 994) with 6091232 elements. Creating vector time with 6128 elements. Creating vector bin with 994 elements. Creating matrix countList (6128 x 994) with 6091232 elements. Creating vector time with 6128 elements. Creating vector bin with 994 elements. Creating vector LCcount with 6128 elements. Creating vector time with 6128 elements. Creating vector transCount with 6128 elements. Creating vector time with 6128 elements. Creating vector nonTransCount with 6128 elements. Creating vector time with 6128 elements. Creating vector ai_mean with 6128 elements. Creating vector time with 6128 elements. Creating vector ai_min with 6128 elements. Creating vector time with 6128 elements. Creating vector ai_max with 6128 elements. Creating vector time with 6128 elements. Creating vector ai_std with 6128 elements. Creating vector time with 6128 elements. Creating vector esd_mean with 6128 elements. Creating vector time with 6128 elements. Creating vector esd_min with 6128 elements. Creating vector time with 6128 elements. Creating vector esd_max with 6128 elements. Creating vector time with 6128 elements. Creating vector esd_std with 6128 elements. Creating vector time with 6128 elements. Creating vector countSum with 6128 elements. Creating vector time with 6128 elements. Creating vector snapshot with 6128 elements. Creating vector time with 6128 elements. Creating vector threshold with 6128 elements. Creating vector time with 6128 elements. Creating vector sampleCount with 6128 elements. Creating vector time with 6128 elements. Creating vector flowCount with 6128 elements. Creating vector time with 6128 elements. Creating vector flowTime with 6128 elements. Creating vector time with 6128 elements. Creating vector bufferStatus with 6128 elements. Creating vector time with 6128 elements. Creating vector laserLevel with 6128 elements. Creating vector time with 6128 elements. Creating vector counter with 6128 elements. Creating vector time with 6128 elements. Creating vector counterPeriod with 6128 elements. Creating vector time with 6128 elements. Creating vector laserControl with 6128 elements. Creating vector time with 6128 elements. Creating vector countUnknownFrameCharacter with 6128 elements. Creating vector time with 6128 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 6128 elements. Creating vector time with 6128 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 6128 elements. Creating vector time with 6128 elements. Creating vector flowSpeed with 6128 elements. Creating vector time with 6128 elements. Creating vector countShortLFrameError with 6128 elements. Creating vector time with 6128 elements. Creating vector countGarbledLFrame with 6128 elements. Creating vector time with 6128 elements. Creating vector cFrameEsecs with 6128 elements. Creating vector time with 6128 elements. Creating vector correctedSampleCountList with 6128 elements. Creating vector time with 6128 elements. Creating vector time with 6128 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010300/2010.300.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.300.00.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_2010.300.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 31 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_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 = 564 Gridding with nix = 1692, iZ = 122 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 transCount nonTransCount LCcount 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 315481 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 315481 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 118877 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 10/27/2010 07:29 to 10/28/2010 08:30 swr = 14.6766 104.3094 417.7018 379.9737 215.6643 75.2408 4.3239 1.5431 1.7858 1.6220 1.7585 1.6530 1.7152 2.0550 2.1142 2.0190 1.7795 2.4549 1.9738 13.2151 117.3911 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2010300_GulperTimes.txt && touch ../results/2010300_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/2010/2010300/2010.300.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010300/2010.300.00/syslog -startEsecs 1288216282.7418 -surveyName Dorado389_2010_300_00_300_00 >> ../results/2010300_GulperTimes.txt Executing: removeGulpDups.py ../results/2010300_GulperTimes.txt Bottle: 0 Time: 1288218949 Depth: 2.2589 Dist: 2.9571 Bottle: 1 Time: 1288236263 Depth: 5.0649 Dist: 21.7702 Bottle: 2 Time: 1288250421 Depth: 5.3242 Dist: 36.9317 Bottle: 3 Time: 1288250438 Depth: 10.712 Dist: 36.9519 Bottle: 4 Time: 1288253808 Depth: 12.4368 Dist: 40.324 Bottle: 5 Time: 1288258382 Depth: 8.2075 Dist: 45.3832 Bottle: 6 Time: 1288278552 Depth: 14.0863 Dist: 68.5368 Bottle: 8 Time: 1288278644 Depth: 16.4536 Dist: 68.6499 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_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_2010_300_00_300_00_2column.png Elapsed time to save image: 11 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_2010_300_00_300_00_biolume.png Elapsed time to save image: 46 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_2010_300_00_300_00_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_2010_300_00_300_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_2column.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2010/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_2010_300_00_300_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_300_00_300_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_300_00_300_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_300_00_300_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_300_00_300_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_300_00_300_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_300_00_300_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_300_00_300_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_300_00_300_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_300_00_300_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_300_00_300_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_300_00_300_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_300_00_300_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_300_00_300_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_300_00_300_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_300_00_300_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2010/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_300_00_300_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_300_00_300_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2010_300_00_300_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00.kml... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_300_00_300_00_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 414) In build_auv_survey (line 522) In AUVprocess_main (line 255)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 21 NaNs found in bbpBlue. Interpolating anyway. 56 NaNs found in bbpRed. Interpolating anyway. 5 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 1258 NaN values in array of lon that is 50355 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 49097 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 49097 are not equal to number of Lat lon points = 50355 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_2010_300_00_300_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00.txt... Copied to /mbari/AUVCTD/surveys/2010/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2010/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... 21 NaNs found in bbpBlue. Interpolating anyway. 56 NaNs found in bbpRed. Interpolating anyway. 5 NaNs found in flRed_uncorr. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2010/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_2010_300_00_300_00.nc... Copied to /mbari/AUVCTD/surveys/2010/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2010/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_300_00_300_00.mat... Copied to /mbari/AUVCTD/surveys/2010/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2010_300_00_300_00 processed" mccann@mbari.org < mail_Dorado389_2010_300_00_300_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.300.00.mat Processing time: 448 seconds