Execution of AUVprocess_main version 1.88 at 2020-11-24T20:38:05Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2020, ['064.10'], '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: 2020.064.10
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/
Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd.cvs/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/2020/2020064/2020.064.10/navigation.nc')
Creating vector time with 381808 elements.
Creating vector mPos_x with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mPos_y with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mDepth with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mGpsNorth with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mGpsEast with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mGpsValid with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mPhi with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mTheta with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mPsi with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mOmega_x with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mOmega_y with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mOmega_z with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mPsaRange with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mAltitude with 381808 elements.
Creating vector time with 381808 elements.
Creating vector multibeamAltitude with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mDvlAltitude with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mEchoAltitude with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mEchoHorizRange with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mEchoAltitudeLast with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mEchoHorizRangeLast with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mEchoNumOfPings with 381808 elements.
Creating vector time with 381808 elements.
Creating vector nadirCnts with 381808 elements.
Creating vector time with 381808 elements.
Creating vector obstacleCnts with 381808 elements.
Creating vector time with 381808 elements.
Creating vector nGoodNadirBeams with 381808 elements.
Creating vector time with 381808 elements.
Creating vector medianNadirBeamNo with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mWaterSpeed with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mDvlValid with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mDvlNewData with 381808 elements.
Creating vector time with 381808 elements.
Creating vector mDeltaT with 381808 elements.
Creating vector time with 381808 elements.
Creating vector nfix with 381808 elements.
Creating vector time with 381808 elements.
Creating vector efix with 381808 elements.
Creating vector time with 381808 elements.
Creating vector filter_north with 381808 elements.
Creating vector time with 381808 elements.
Creating vector filter_east with 381808 elements.
Creating vector time with 381808 elements.
Creating vector filter_depth with 381808 elements.
Creating vector time with 381808 elements.
Creating vector north_current with 381808 elements.
Creating vector time with 381808 elements.
Creating vector east_current with 381808 elements.
Creating vector time with 381808 elements.
Creating vector speed_bias with 381808 elements.
Creating vector time with 381808 elements.
Creating vector heading_bias with 381808 elements.
Creating vector time with 381808 elements.
Creating vector latitude with 381808 elements.
Creating vector time with 381808 elements.
Creating vector longitude with 381808 elements.
Creating vector time with 381808 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/navigation.nc');
processNav(): median of positive valued depths = 33.6043
processNav(): Finding depths less than 235.23 and times > 0
processNav(): length(Nav.depth) = 381808
processNav(): length(gindx)     = 381808
 
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/2020/2020064/2020.064.10/gps.nc')
Creating vector time with 6520 elements.
Creating vector hours with 6520 elements.
Creating vector time with 6520 elements.
Creating vector minutes with 6520 elements.
Creating vector time with 6520 elements.
Creating vector seconds with 6520 elements.
Creating vector time with 6520 elements.
Creating vector centiSeconds with 6520 elements.
Creating vector time with 6520 elements.
Creating vector latitude with 6520 elements.
Creating vector time with 6520 elements.
Creating vector longitude with 6520 elements.
Creating vector time with 6520 elements.
Creating vector quality with 6520 elements.
Creating vector time with 6520 elements.
Creating vector numberOfSatellites with 6520 elements.
Creating vector time with 6520 elements.
Creating vector hdop with 6520 elements.
Creating vector time with 6520 elements.
Creating vector antennaHeight with 6520 elements.
Creating vector time with 6520 elements.
Creating vector geoHeight with 6520 elements.
Creating vector time with 6520 elements.
Creating vector dgpsDataAge with 6520 elements.
Creating vector time with 6520 elements.
Creating vector dgpsRSID with 6520 elements.
Creating vector time with 6520 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/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/2020/2020064/2020.064.10/parosci.nc')
Creating vector time with 760304 elements.
Creating vector depth with 760304 elements.
Creating vector time with 760304 elements.
Creating vector temp with 760304 elements.
Creating vector time with 760304 elements.
Creating vector pressure with 760304 elements.
Creating vector time with 760304 elements.
Creating vector temp_period with 760304 elements.
Creating vector time with 760304 elements.
Creating vector pres_period with 760304 elements.
Creating vector time with 760304 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.2516 max(Depth.data) = 203.0262
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.2516 max(Depth.data) = 203.0262
 
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/2020/2020064/2020.064.10/hydroscatlog.nc')
Creating vector time with 305413 elements.
Creating vector Seconds with 305413 elements.
Creating vector time with 305413 elements.
Creating vector HundrethsOfSeconds with 305413 elements.
Creating vector time with 305413 elements.
Creating vector Snorm1 with 305413 elements.
Creating vector time with 305413 elements.
Creating vector Snorm2 with 305413 elements.
Creating vector time with 305413 elements.
Creating vector Snorm3 with 305413 elements.
Creating vector time with 305413 elements.
Creating vector Gain_Status_1 with 305413 elements.
Creating vector time with 305413 elements.
Creating vector Gain_Status_2 with 305413 elements.
Creating vector time with 305413 elements.
Creating vector Gain_Status_3 with 305413 elements.
Creating vector time with 305413 elements.
Creating vector RawDepthValue with 305413 elements.
Creating vector time with 305413 elements.
Creating vector RawTempValue with 305413 elements.
Creating vector time with 305413 elements.
Creating vector Temperature with 305413 elements.
Creating vector time with 305413 elements.
Creating vector ErrorValue with 305413 elements.
Creating vector time with 305413 elements.
Creating vector bb470 with 305413 elements.
Creating vector time with 305413 elements.
Creating vector bb676 with 305413 elements.
Creating vector time with 305413 elements.
Creating vector fl676u with 305413 elements.
Creating vector time with 305413 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/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/2020/2020064/2020.064.10/ctdDriver.nc')
Creating vector time with 305347 elements.
Creating vector conductivity with 305347 elements.
Creating vector time with 305347 elements.
Creating vector temperature with 305347 elements.
Creating vector time with 305347 elements.
Creating vector cond_frequency with 305347 elements.
Creating vector time with 305347 elements.
Creating vector temp_frequency with 305347 elements.
Creating vector time with 305347 elements.
Creating vector spare with 305347 elements.
Creating vector time with 305347 elements.
Creating vector humidity with 305347 elements.
Creating vector time with 305347 elements.
Creating vector flow1 with 305347 elements.
Creating vector time with 305347 elements.
Creating vector CDOM with 305347 elements.
Creating vector time with 305347 elements.
Creating vector dissolvedO2 with 305347 elements.
Creating vector time with 305347 elements.
Creating vector salinity with 305347 elements.
Creating vector time with 305347 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/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/2020/2020064/2020.064.10/ctdDriver2.nc')
Creating vector time with 305478 elements.
Creating vector conductivity with 305478 elements.
Creating vector time with 305478 elements.
Creating vector temperature with 305478 elements.
Creating vector time with 305478 elements.
Creating vector cond_frequency with 305478 elements.
Creating vector time with 305478 elements.
Creating vector temp_frequency with 305478 elements.
Creating vector time with 305478 elements.
Creating vector flow2 with 305478 elements.
Creating vector time with 305478 elements.
Creating vector spare with 305478 elements.
Creating vector time with 305478 elements.
Creating vector salinity with 305478 elements.
Creating vector time with 305478 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/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/2020/2020064/2020.064.10/isuslog.nc')
Creating vector time with 59599 elements.
Creating vector isusNitrate with 59599 elements.
Creating vector time with 59599 elements.
Creating vector isusTemp with 59599 elements.
Creating vector time with 59599 elements.
Creating vector isusQuality with 59599 elements.
Creating vector time with 59599 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/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 71)
  In processBiolume (line 21)
  In processAUVmission (line 220)
  In AUVprocess_main (line 227)] 
[Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 71)
  In processBiolume (line 22)
  In processAUVmission (line 220)
  In AUVprocess_main (line 227)] 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/biolume.nc')
Creating vector time with 75108 elements.
Creating vector rrr with 75108 elements.
Creating vector time with 75108 elements.
Creating vector cal_striing with 75108 elements.
Creating vector time with 75108 elements.
Creating vector avg_biolume with 75108 elements.
Creating vector time with 75108 elements.
Creating vector pump with 75108 elements.
Creating vector time with 75108 elements.
Creating vector system_voltage with 75108 elements.
Creating vector time with 75108 elements.
Creating vector flow with 75108 elements.
Creating vector time with 75108 elements.
Creating vector HV with 75108 elements.
Creating vector time with 75108 elements.
Creating vector reserved with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_0 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_1 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_2 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_3 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_4 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_5 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_6 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_7 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_8 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_9 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_10 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_11 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_12 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_13 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_14 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_15 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_16 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_17 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_18 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_19 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_20 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_21 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_22 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_23 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_24 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_25 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_26 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_27 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_28 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_29 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_30 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_31 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_32 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_33 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_34 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_35 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_36 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_37 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_38 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_39 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_40 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_41 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_42 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_43 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_44 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_45 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_46 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_47 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_48 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_49 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_50 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_51 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_52 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_53 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_54 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_55 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_56 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_57 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_58 with 75108 elements.
Creating vector time with 75108 elements.
Creating vector raw_59 with 75108 elements.
Creating vector time with 75108 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/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/2020/2020064/2020.064.10/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (7275 x 994) with 7231350 elements.
Creating vector time with 7275 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (7275 x 994) with 7231350 elements.
Creating vector time with 7275 elements.
Creating vector bin with 994 elements.
Creating matrix countList (7275 x 994) with 7231350 elements.
Creating vector time with 7275 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 7275 elements.
Creating vector time with 7275 elements.
Creating vector transCount with 7275 elements.
Creating vector time with 7275 elements.
Creating vector nonTransCount with 7275 elements.
Creating vector time with 7275 elements.
Creating vector ai_mean with 7275 elements.
Creating vector time with 7275 elements.
Creating vector ai_min with 7275 elements.
Creating vector time with 7275 elements.
Creating vector ai_max with 7275 elements.
Creating vector time with 7275 elements.
Creating vector ai_std with 7275 elements.
Creating vector time with 7275 elements.
Creating vector esd_mean with 7275 elements.
Creating vector time with 7275 elements.
Creating vector esd_min with 7275 elements.
Creating vector time with 7275 elements.
Creating vector esd_max with 7275 elements.
Creating vector time with 7275 elements.
Creating vector esd_std with 7275 elements.
Creating vector time with 7275 elements.
Creating vector countSum with 7275 elements.
Creating vector time with 7275 elements.
Creating vector snapshot with 7275 elements.
Creating vector time with 7275 elements.
Creating vector threshold with 7275 elements.
Creating vector time with 7275 elements.
Creating vector sampleCount with 7275 elements.
Creating vector time with 7275 elements.
Creating vector flowCount with 7275 elements.
Creating vector time with 7275 elements.
Creating vector flowTime with 7275 elements.
Creating vector time with 7275 elements.
Creating vector bufferStatus with 7275 elements.
Creating vector time with 7275 elements.
Creating vector laserLevel with 7275 elements.
Creating vector time with 7275 elements.
Creating vector counter with 7275 elements.
Creating vector time with 7275 elements.
Creating vector counterPeriod with 7275 elements.
Creating vector time with 7275 elements.
Creating vector laserControl with 7275 elements.
Creating vector time with 7275 elements.
Creating vector countUnknownFrameCharacter with 7275 elements.
Creating vector time with 7275 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7275 elements.
Creating vector time with 7275 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7275 elements.
Creating vector time with 7275 elements.
Creating vector flowSpeed with 7275 elements.
Creating vector time with 7275 elements.
Creating vector countShortLFrameError with 7275 elements.
Creating vector time with 7275 elements.
Creating vector countGarbledLFrame with 7275 elements.
Creating vector time with 7275 elements.
Creating vector cFrameEsecs with 7275 elements.
Creating vector time with 7275 elements.
Creating vector correctedSampleCountList with 7275 elements.
Creating vector time with 7275 elements.
Creating vector time with 7275 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020064/2020.064.10/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.064.10.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.cvs/src/matlab/doradosdp/results/Dorado389_2020.064.10.mat

has_par2 =

     0

Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 26 segments.
[Warning: MATLAB has disabled some advanced graphics rendering features by
switching to software OpenGL. For more information, click <a
href="matlab:opengl('problems')">here</a>.] 
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10.mat
Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10.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 = 336 Gridding with nix = 1008, iZ = 403
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 254424 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 <n>f or <n>d, with w to indicate swab
grdtrack: Processing input grid(s)
grdtrack: Output 1 columns via binary records using format f
grdtrack: Sampled 254424 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 140703 elements.

ds = 

  cfdataset with properties:

       netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset]
    variables: {16x1 cell}

SWR data read from OPeNDAP has time range: 03/04/2020 10:30  to 03/05/2020 09:29 

swr =

  537.4214
  665.2898
  738.5194
  572.7943
  399.1294
  305.5915
  146.3541
   33.4253
    3.4325
    2.8333
    3.3667
    3.0333
    3.1336
    3.1325
    2.7004
    3.1338
    2.9331
    2.8664
    2.9007
    2.9658
    3.8086
   23.8265
   56.9382
  173.0983

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2020064_GulperTimes.txt && touch ../results/2020064_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/2020/2020064/2020.064.10/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2020/2020064/2020.064.10/syslog -startEsecs 1583353928.979 -surveyName Dorado389_2020_064_10_064_10 >> ../results/2020064_GulperTimes.txt
Executing: removeGulpDups.py ../results/2020064_GulperTimes.txt
Bottle: 0 Time: 1583355193.3724 Depth: 200.0721 Dist: 1.2214
Bottle: 1 Time: 1583355324.7734 Depth: 149.9196 Dist: 1.379
Bottle: 2 Time: 1583355447.175 Depth: 99.917 Dist: 1.5511
Bottle: 3 Time: 1583355501.3713 Depth: 79.918 Dist: 1.6305
Bottle: 4 Time: 1583355560.5772 Depth: 59.9658 Dist: 1.7265
Bottle: 5 Time: 1583355616.9734 Depth: 39.9434 Dist: 1.8052
Bottle: 6 Time: 1583355646.9713 Depth: 29.982 Dist: 1.839
Bottle: 7 Time: 1583355678.7791 Depth: 19.9983 Dist: 1.8695
Bottle: 8 Time: 1583355713.1768 Depth: 9.9487 Dist: 1.9058
Bottle: 9 Time: 1583356151.5767 Depth: 0.013227 Dist: 2.0093
Bottle: 10 Time: 1583385003.3803 Depth: 200.0332 Dist: 35.9458
Bottle: 11 Time: 1583385133.5713 Depth: 149.9558 Dist: 36.0908
Bottle: 12 Time: 1583385249.9734 Depth: 99.9403 Dist: 36.2034
Bottle: 13 Time: 1583385302.7798 Depth: 79.9326 Dist: 36.2526
Bottle: 14 Time: 1583385355.1762 Depth: 59.9915 Dist: 36.3037
Bottle: 15 Time: 1583385413.5722 Depth: 39.9249 Dist: 36.3754
Bottle: 16 Time: 1583385443.5801 Depth: 29.932 Dist: 36.407
Bottle: 17 Time: 1583385475.3779 Depth: 19.9653 Dist: 36.4326
Bottle: 18 Time: 1583385503.576 Depth: 9.9284 Dist: 36.4593
Bottle: 19 Time: 1583385540.5735 Depth: -0.096807 Dist: 36.4981
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_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.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_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.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_biolume.png
Elapsed time to save image: 43 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.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_lopc.png
Elapsed time to save image: 13 seconds
 
 
*************************************************************************
Calling plot_survey_stats to produce histogram and profile statistics plots...
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_2column.png...
Copied to /mbari/AUVCTD/surveys/2020/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_biolume.png...
Copied to /mbari/AUVCTD/surveys/2020/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_lopc.png...
Copied to /mbari/AUVCTD/surveys/2020/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2020/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2020/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2020/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2020/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2020/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2020/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2020/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Optical_Backscatter_420_nm.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2020/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2020/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Chlorophyll_Fluorescence.kml (deflated 92%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2020/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2020/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2020/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
Creating Dorado389_2020_064_10_064_10.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10.kml...
Copied to /mbari/AUVCTD/surveys/2020/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_064_10_064_10_LOPC_Total_Count.kml'
not found.] 
[> In create_data_products (line 419)
  In build_auv_survey (line 530)
  In AUVprocess_main (line 257)] 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
11 NaNs found in bbpRed.  Interpolating anyway.
Encountered 19897 NaN values in array of lon that is 59599 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 <n>f or <n>d, with w to indicate swab
grdtrack: Processing input grid(s)
grdtrack: Output 1 columns via binary records using format f
grdtrack: Sampled 39702 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 39702 are not equal to number of Lat lon points = 59599
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.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10.txt
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10.txt...
Copied to /mbari/AUVCTD/surveys/2020/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2020/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
11 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_decim.nc...
Copied to /mbari/AUVCTD/surveys/2020/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing netCDF file ...
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10.nc...
Copied to /mbari/AUVCTD/surveys/2020/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2020/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_064_10_064_10.mat...
Copied to /mbari/AUVCTD/surveys/2020/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
permalink_url.sh http://dods.mbari.org/cgi-bin/nph-nc/data/auvctd/surveys/2020/netcdf/Dorado389_2020_064_10_064_10.nc
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2020_064_10_064_10 processed" mccann@mbari.org < mail_Dorado389_2020_064_10_064_10.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.064.10.mat
Processing time: 264 seconds