Execution of AUVprocess_main version 1.86 at 2018-05-24T21:03:12Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2013, ['301.02'], '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: 2013.301.02 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/ 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/2013/2013301/2013.301.02/navigation.nc') Creating vector time with 1555 elements. Creating vector mPos_x with 1555 elements. Creating vector time with 1555 elements. Creating vector mPos_y with 1555 elements. Creating vector time with 1555 elements. Creating vector mDepth with 1555 elements. Creating vector time with 1555 elements. Creating vector mGpsNorth with 1555 elements. Creating vector time with 1555 elements. Creating vector mGpsEast with 1555 elements. Creating vector time with 1555 elements. Creating vector mGpsValid with 1555 elements. Creating vector time with 1555 elements. Creating vector mPhi with 1555 elements. Creating vector time with 1555 elements. Creating vector mTheta with 1555 elements. Creating vector time with 1555 elements. Creating vector mPsi with 1555 elements. Creating vector time with 1555 elements. Creating vector mOmega_x with 1555 elements. Creating vector time with 1555 elements. Creating vector mOmega_y with 1555 elements. Creating vector time with 1555 elements. Creating vector mOmega_z with 1555 elements. Creating vector time with 1555 elements. Creating vector mPsaRange with 1555 elements. Creating vector time with 1555 elements. Creating vector mAltitude with 1555 elements. Creating vector time with 1555 elements. Creating vector mDvlAltitude with 1555 elements. Creating vector time with 1555 elements. Creating vector mEchoAltitude with 1555 elements. Creating vector time with 1555 elements. Creating vector mEchoHorizRange with 1555 elements. Creating vector time with 1555 elements. Creating vector mEchoAltitudeLast with 1555 elements. Creating vector time with 1555 elements. Creating vector mEchoHorizRangeLast with 1555 elements. Creating vector time with 1555 elements. Creating vector mEchoNumOfPings with 1555 elements. Creating vector time with 1555 elements. Creating vector mWaterSpeed with 1555 elements. Creating vector time with 1555 elements. Creating vector mDvlValid with 1555 elements. Creating vector time with 1555 elements. Creating vector mDvlNewData with 1555 elements. Creating vector time with 1555 elements. Creating vector mDeltaT with 1555 elements. Creating vector time with 1555 elements. Creating vector nfix with 1555 elements. Creating vector time with 1555 elements. Creating vector efix with 1555 elements. Creating vector time with 1555 elements. Creating vector filter_north with 1555 elements. Creating vector time with 1555 elements. Creating vector filter_east with 1555 elements. Creating vector time with 1555 elements. Creating vector filter_depth with 1555 elements. Creating vector time with 1555 elements. Creating vector north_current with 1555 elements. Creating vector time with 1555 elements. Creating vector east_current with 1555 elements. Creating vector time with 1555 elements. Creating vector speed_bias with 1555 elements. Creating vector time with 1555 elements. Creating vector heading_bias with 1555 elements. Creating vector time with 1555 elements. Creating vector latitude with 1555 elements. Creating vector time with 1555 elements. Creating vector longitude with 1555 elements. Creating vector time with 1555 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/navigation.nc'); Bypassing Nav QC depth check processNav(): median of positive valued depths = NaN processNav(): Finding depths less than 1250 and times > 0 processNav(): length(Nav.depth) = 1555 processNav(): length(gindx) = 1555 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/2013/2013301/2013.301.02/gps.nc') Creating vector time with 349 elements. Creating vector hours with 349 elements. Creating vector time with 349 elements. Creating vector minutes with 349 elements. Creating vector time with 349 elements. Creating vector seconds with 349 elements. Creating vector time with 349 elements. Creating vector centiSeconds with 349 elements. Creating vector time with 349 elements. Creating vector latitude with 349 elements. Creating vector time with 349 elements. Creating vector longitude with 349 elements. Creating vector time with 349 elements. Creating vector quality with 349 elements. Creating vector time with 349 elements. Creating vector numberOfSatellites with 349 elements. Creating vector time with 349 elements. Creating vector hdop with 349 elements. Creating vector time with 349 elements. Creating vector antennaHeight with 349 elements. Creating vector time with 349 elements. Creating vector geoHeight with 349 elements. Creating vector time with 349 elements. Creating vector dgpsDataAge with 349 elements. Creating vector time with 349 elements. Creating vector dgpsRSID with 349 elements. Creating vector time with 349 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/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/2013/2013301/2013.301.02/parosci.nc') Creating vector time with 3407 elements. Creating vector depth with 3407 elements. Creating vector time with 3407 elements. Creating vector temp with 3407 elements. Creating vector time with 3407 elements. Creating vector pressure with 3407 elements. Creating vector time with 3407 elements. Creating vector temp_period with 3407 elements. Creating vector time with 3407 elements. Creating vector pres_period with 3407 elements. Creating vector time with 3407 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.24469 max(Depth.data) = 0.064877 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.24469 max(Depth.data) = 0.064877 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/2013/2013301/2013.301.02/hydroscatlog.nc') Creating vector time with 1369 elements. Creating vector Seconds with 1369 elements. Creating vector time with 1369 elements. Creating vector HundrethsOfSeconds with 1369 elements. Creating vector time with 1369 elements. Creating vector Snorm1 with 1369 elements. Creating vector time with 1369 elements. Creating vector Snorm2 with 1369 elements. Creating vector time with 1369 elements. Creating vector Snorm3 with 1369 elements. Creating vector time with 1369 elements. Creating vector Gain_Status_1 with 1369 elements. Creating vector time with 1369 elements. Creating vector Gain_Status_2 with 1369 elements. Creating vector time with 1369 elements. Creating vector Gain_Status_3 with 1369 elements. Creating vector time with 1369 elements. Creating vector RawDepthValue with 1369 elements. Creating vector time with 1369 elements. Creating vector RawTempValue with 1369 elements. Creating vector time with 1369 elements. Creating vector Temperature with 1369 elements. Creating vector time with 1369 elements. Creating vector ErrorValue with 1369 elements. Creating vector time with 1369 elements. Creating vector bb470 with 1369 elements. Creating vector time with 1369 elements. Creating vector bb676 with 1369 elements. Creating vector time with 1369 elements. Creating vector fl676u with 1369 elements. Creating vector time with 1369 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/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/2013/2013301/2013.301.02/ctdDriver.nc') Creating vector time with 1286 elements. Creating vector conductivity with 1286 elements. Creating vector time with 1286 elements. Creating vector temperature with 1286 elements. Creating vector time with 1286 elements. Creating vector cond_frequency with 1286 elements. Creating vector time with 1286 elements. Creating vector temp_frequency with 1286 elements. Creating vector time with 1286 elements. Creating vector spare with 1286 elements. Creating vector time with 1286 elements. Creating vector humidity with 1286 elements. Creating vector time with 1286 elements. Creating vector flow1 with 1286 elements. Creating vector time with 1286 elements. Creating vector CDOM with 1286 elements. Creating vector time with 1286 elements. Creating vector dissolvedO2 with 1286 elements. Creating vector time with 1286 elements. Creating vector salinity with 1286 elements. Creating vector time with 1286 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/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/2013/2013301/2013.301.02/ctdDriver2.nc') Creating vector time with 1286 elements. Creating vector conductivity with 1286 elements. Creating vector time with 1286 elements. Creating vector temperature with 1286 elements. Creating vector time with 1286 elements. Creating vector cond_frequency with 1286 elements. Creating vector time with 1286 elements. Creating vector temp_frequency with 1286 elements. Creating vector time with 1286 elements. Creating vector flow2 with 1286 elements. Creating vector time with 1286 elements. Creating vector spare with 1286 elements. Creating vector time with 1286 elements. Creating vector salinity with 1286 elements. Creating vector time with 1286 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/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/2013/2013301/2013.301.02/isuslog.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/isuslog.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/isuslog.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/isuslog.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting ISUS structure to NaN values. 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/2013/2013301/2013.301.02/biolume.nc') Creating vector time with 343 elements. Creating vector rrr with 343 elements. Creating vector time with 343 elements. Creating vector cal_striing with 343 elements. Creating vector time with 343 elements. Creating vector avg_biolume with 343 elements. Creating vector time with 343 elements. Creating vector pump with 343 elements. Creating vector time with 343 elements. Creating vector system_voltage with 343 elements. Creating vector time with 343 elements. Creating vector flow with 343 elements. Creating vector time with 343 elements. Creating vector HV with 343 elements. Creating vector time with 343 elements. Creating vector reserved with 343 elements. Creating vector time with 343 elements. Creating vector raw_0 with 343 elements. Creating vector time with 343 elements. Creating vector raw_1 with 343 elements. Creating vector time with 343 elements. Creating vector raw_2 with 343 elements. Creating vector time with 343 elements. Creating vector raw_3 with 343 elements. Creating vector time with 343 elements. Creating vector raw_4 with 343 elements. Creating vector time with 343 elements. Creating vector raw_5 with 343 elements. Creating vector time with 343 elements. Creating vector raw_6 with 343 elements. Creating vector time with 343 elements. Creating vector raw_7 with 343 elements. Creating vector time with 343 elements. Creating vector raw_8 with 343 elements. Creating vector time with 343 elements. Creating vector raw_9 with 343 elements. Creating vector time with 343 elements. Creating vector raw_10 with 343 elements. Creating vector time with 343 elements. Creating vector raw_11 with 343 elements. Creating vector time with 343 elements. Creating vector raw_12 with 343 elements. Creating vector time with 343 elements. Creating vector raw_13 with 343 elements. Creating vector time with 343 elements. Creating vector raw_14 with 343 elements. Creating vector time with 343 elements. Creating vector raw_15 with 343 elements. Creating vector time with 343 elements. Creating vector raw_16 with 343 elements. Creating vector time with 343 elements. Creating vector raw_17 with 343 elements. Creating vector time with 343 elements. Creating vector raw_18 with 343 elements. Creating vector time with 343 elements. Creating vector raw_19 with 343 elements. Creating vector time with 343 elements. Creating vector raw_20 with 343 elements. Creating vector time with 343 elements. Creating vector raw_21 with 343 elements. Creating vector time with 343 elements. Creating vector raw_22 with 343 elements. Creating vector time with 343 elements. Creating vector raw_23 with 343 elements. Creating vector time with 343 elements. Creating vector raw_24 with 343 elements. Creating vector time with 343 elements. Creating vector raw_25 with 343 elements. Creating vector time with 343 elements. Creating vector raw_26 with 343 elements. Creating vector time with 343 elements. Creating vector raw_27 with 343 elements. Creating vector time with 343 elements. Creating vector raw_28 with 343 elements. Creating vector time with 343 elements. Creating vector raw_29 with 343 elements. Creating vector time with 343 elements. Creating vector raw_30 with 343 elements. Creating vector time with 343 elements. Creating vector raw_31 with 343 elements. Creating vector time with 343 elements. Creating vector raw_32 with 343 elements. Creating vector time with 343 elements. Creating vector raw_33 with 343 elements. Creating vector time with 343 elements. Creating vector raw_34 with 343 elements. Creating vector time with 343 elements. Creating vector raw_35 with 343 elements. Creating vector time with 343 elements. Creating vector raw_36 with 343 elements. Creating vector time with 343 elements. Creating vector raw_37 with 343 elements. Creating vector time with 343 elements. Creating vector raw_38 with 343 elements. Creating vector time with 343 elements. Creating vector raw_39 with 343 elements. Creating vector time with 343 elements. Creating vector raw_40 with 343 elements. Creating vector time with 343 elements. Creating vector raw_41 with 343 elements. Creating vector time with 343 elements. Creating vector raw_42 with 343 elements. Creating vector time with 343 elements. Creating vector raw_43 with 343 elements. Creating vector time with 343 elements. Creating vector raw_44 with 343 elements. Creating vector time with 343 elements. Creating vector raw_45 with 343 elements. Creating vector time with 343 elements. Creating vector raw_46 with 343 elements. Creating vector time with 343 elements. Creating vector raw_47 with 343 elements. Creating vector time with 343 elements. Creating vector raw_48 with 343 elements. Creating vector time with 343 elements. Creating vector raw_49 with 343 elements. Creating vector time with 343 elements. Creating vector raw_50 with 343 elements. Creating vector time with 343 elements. Creating vector raw_51 with 343 elements. Creating vector time with 343 elements. Creating vector raw_52 with 343 elements. Creating vector time with 343 elements. Creating vector raw_53 with 343 elements. Creating vector time with 343 elements. Creating vector raw_54 with 343 elements. Creating vector time with 343 elements. Creating vector raw_55 with 343 elements. Creating vector time with 343 elements. Creating vector raw_56 with 343 elements. Creating vector time with 343 elements. Creating vector raw_57 with 343 elements. Creating vector time with 343 elements. Creating vector raw_58 with 343 elements. Creating vector time with 343 elements. Creating vector raw_59 with 343 elements. Creating vector time with 343 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/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/2013/2013301/2013.301.02/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (33 x 994) with 32802 elements. Creating vector time with 33 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (33 x 994) with 32802 elements. Creating vector time with 33 elements. Creating vector bin with 994 elements. Creating matrix countList (33 x 994) with 32802 elements. Creating vector time with 33 elements. Creating vector bin with 994 elements. Creating vector LCcount with 33 elements. Creating vector time with 33 elements. Creating vector transCount with 33 elements. Creating vector time with 33 elements. Creating vector nonTransCount with 33 elements. Creating vector time with 33 elements. Creating vector ai_mean with 33 elements. Creating vector time with 33 elements. Creating vector ai_min with 33 elements. Creating vector time with 33 elements. Creating vector ai_max with 33 elements. Creating vector time with 33 elements. Creating vector ai_std with 33 elements. Creating vector time with 33 elements. Creating vector esd_mean with 33 elements. Creating vector time with 33 elements. Creating vector esd_min with 33 elements. Creating vector time with 33 elements. Creating vector esd_max with 33 elements. Creating vector time with 33 elements. Creating vector esd_std with 33 elements. Creating vector time with 33 elements. Creating vector countSum with 33 elements. Creating vector time with 33 elements. Creating vector snapshot with 33 elements. Creating vector time with 33 elements. Creating vector threshold with 33 elements. Creating vector time with 33 elements. Creating vector sampleCount with 33 elements. Creating vector time with 33 elements. Creating vector flowCount with 33 elements. Creating vector time with 33 elements. Creating vector flowTime with 33 elements. Creating vector time with 33 elements. Creating vector bufferStatus with 33 elements. Creating vector time with 33 elements. Creating vector laserLevel with 33 elements. Creating vector time with 33 elements. Creating vector counter with 33 elements. Creating vector time with 33 elements. Creating vector counterPeriod with 33 elements. Creating vector time with 33 elements. Creating vector laserControl with 33 elements. Creating vector time with 33 elements. Creating vector countUnknownFrameCharacter with 33 elements. Creating vector time with 33 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 33 elements. Creating vector time with 33 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 33 elements. Creating vector time with 33 elements. Creating vector flowSpeed with 33 elements. Creating vector time with 33 elements. Creating vector countShortLFrameError with 33 elements. Creating vector time with 33 elements. Creating vector countGarbledLFrame with 33 elements. Creating vector time with 33 elements. Creating vector cFrameEsecs with 33 elements. Creating vector time with 33 elements. Creating vector correctedSampleCountList with 33 elements. Creating vector time with 33 elements. Creating vector time with 33 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013301/2013.301.02/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.301.02.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_2013.301.02.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... matchDVLtoGPS(): No underwater portion identified with tDiffCrit = 720 matchDVLtoGPS(): almostMaxDiff = 0.4499 not big enough. Probably stayed at surface the whole mission. matchDVLtoGPS(): Yes. max(depth.nav) = 0.14877 Entire mission at surface. Looping over 0 segments. Current plot held [Warning: Ignoring extra legend entries.] [> In legend>set_children_and_strings (line 646) In legend>make_legend (line 316) In legend (line 259) In create_data_products (line 82) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02.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 = 2 Gridding with nix = 6, iZ = 3 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 Only one good point - NaNing the gN array. BL BLflow LOPC Only one good point or fewer - NaNing the gLOPCcount array. - NaNing the gLOPCtransCount array. - NaNing the gLOPCnonTransCount array. - NaNing the gLOPCLCcount array. Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN No valid data for gN cvarname = gF cvarname = gB420 cvarname = gB700 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount No valid data for gLOPCcount cvarname = gLOPCtransCount No valid data for gLOPCtransCount cvarname = gLOPCnonTransCount No valid data for gLOPCnonTransCount cvarname = gLOPCLCcount No valid data for gLOPCLCcount Encountered 0 NaN values in array of lon that is 349 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 349 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 118898 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 10/28/2013 06:30 to 10/28/2013 08:30 swr = 2.5405 5.9853 47.1321 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2013301_GulperTimes.txt && touch ../results/2013301_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/2013/2013301/2013.301.02/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013301/2013.301.02/syslog -startEsecs 1382974104.3379 -surveyName Dorado389_2013_301_02_301_02 >> ../results/2013301_GulperTimes.txt Executing: removeGulpDups.py ../results/2013301_GulperTimes.txt Bottle: 6 Time: 1382974284 Depth: -0.0041376 Dist: 0.048033 Bottle: 3 Time: 1382974284 Depth: -0.0041376 Dist: 0.048033 Bottle: 7 Time: 1382974284 Depth: -0.0041376 Dist: 0.048033 Bottle: 9 Time: 1382974284 Depth: -0.0041376 Dist: 0.048033 Bottle: 2 Time: 1382974284 Depth: -0.0041376 Dist: 0.048033 Bottle: 8 Time: 1382974284 Depth: -0.0041376 Dist: 0.048033 Bottle: 1 Time: 1382974284 Depth: -0.0041376 Dist: 0.048033 Bottle: 4 Time: 1382974284 Depth: -0.0041376 Dist: 0.048033 Bottle: 0 Time: 1382974284 Depth: -0.0041376 Dist: 0.048033 Bottle: 5 Time: 1382974284 Depth: -0.0041376 Dist: 0.048033 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_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 2Column contouring gridded variable gT [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 852) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gS [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 852) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gN [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 852) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gO [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 852) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gB420 [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 852) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gB700 [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 852) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gF [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 852) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gBL [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 852) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_2column.png Elapsed time to save image: 3 seconds Biolume contouring gridded variable gD Biolume contouring gridded variable gT [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1181) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Biolume contouring gridded variable gS [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1181) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Biolume contouring gridded variable gN [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1181) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Biolume contouring gridded variable gO [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1181) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Biolume contouring gridded variable gB420 [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1181) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Biolume contouring gridded variable gB700 [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1181) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Biolume contouring gridded variable gF [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1181) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Biolume contouring gridded variable gBL [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1181) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_biolume.png Elapsed time to save image: 16 seconds 2Column contouring gridded variable gLOPCcount [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1497) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gLOPCtransCount [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1497) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gLOPCnonTransCount [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1497) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gLOPCLCcount [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1497) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gT [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1497) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gB420 [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1497) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gB700 [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1497) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gF [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1497) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 2Column contouring gridded variable gBL [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 1497) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_lopc.png Elapsed time to save image: 3 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_2013_301_02_301_02_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_2column.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_biolume.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_lopc.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2013/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Temperature.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2013/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Salinity.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2013/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); length(v_esecs(gindx)) = which is less than 2. Not processing. updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2013/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Oxygen.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2013/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Optical_Backscatter_420_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2013/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Optical_Backscatter_700_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2013/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Chlorophyll_Fluorescence.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2013/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Bioluminescence.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2013/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 create .kmz for LOPC Total Count Creating Dorado389_2013_301_02_301_02.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02.kml... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_301_02_301_02_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_2013_301_02_301_02.mat ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in bbpRed. Interpolating anyway. Encountered 0 NaN values in array of lon that is 129 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 129 points from grid Monterey25.grd (2876 x 2447) Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02.txt... Copied to /mbari/AUVCTD/surveys/2013/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2013/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_decim.nc... Copied to /mbari/AUVCTD/surveys/2013/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_2013_301_02_301_02.nc... Copied to /mbari/AUVCTD/surveys/2013/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02_gridded.mat... Copied to /mbari/AUVCTD/surveys/2013/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_301_02_301_02.mat... Copied to /mbari/AUVCTD/surveys/2013/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2013_301_02_301_02 processed" mccann@mbari.org < mail_Dorado389_2013_301_02_301_02.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.301.02.mat Processing time: 21 seconds