Execution of AUVprocess_main version 1.88 at 2020-08-26T22:28:30Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2017, ['297.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd2')
 
*************************************************************************
Processing data from SSDS via DODS server
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2017.297.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/
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/2017/2017297/2017.297.00/navigation.nc')
Creating vector time with 394649 elements.
Creating vector mPos_x with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mPos_y with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mDepth with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mGpsNorth with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mGpsEast with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mGpsValid with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mPhi with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mTheta with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mPsi with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mOmega_x with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mOmega_y with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mOmega_z with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mPsaRange with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mAltitude with 394649 elements.
Creating vector time with 394649 elements.
Creating vector multibeamAltitude with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mDvlAltitude with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mEchoAltitude with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mEchoHorizRange with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mEchoAltitudeLast with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mEchoHorizRangeLast with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mEchoNumOfPings with 394649 elements.
Creating vector time with 394649 elements.
Creating vector nadirCnts with 394649 elements.
Creating vector time with 394649 elements.
Creating vector obstacleCnts with 394649 elements.
Creating vector time with 394649 elements.
Creating vector nGoodNadirBeams with 394649 elements.
Creating vector time with 394649 elements.
Creating vector medianNadirBeamNo with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mWaterSpeed with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mDvlValid with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mDvlNewData with 394649 elements.
Creating vector time with 394649 elements.
Creating vector mDeltaT with 394649 elements.
Creating vector time with 394649 elements.
Creating vector nfix with 394649 elements.
Creating vector time with 394649 elements.
Creating vector efix with 394649 elements.
Creating vector time with 394649 elements.
Creating vector filter_north with 394649 elements.
Creating vector time with 394649 elements.
Creating vector filter_east with 394649 elements.
Creating vector time with 394649 elements.
Creating vector filter_depth with 394649 elements.
Creating vector time with 394649 elements.
Creating vector north_current with 394649 elements.
Creating vector time with 394649 elements.
Creating vector east_current with 394649 elements.
Creating vector time with 394649 elements.
Creating vector speed_bias with 394649 elements.
Creating vector time with 394649 elements.
Creating vector heading_bias with 394649 elements.
Creating vector time with 394649 elements.
Creating vector latitude with 394649 elements.
Creating vector time with 394649 elements.
Creating vector longitude with 394649 elements.
Creating vector time with 394649 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/navigation.nc');
processNav(): median of positive valued depths = 33.1846
processNav(): Finding depths less than 232.2922 and times > 0
processNav(): length(Nav.depth) = 394649
processNav(): length(gindx)     = 394649
 
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/2017/2017297/2017.297.00/gps.nc')
Creating vector time with 8971 elements.
Creating vector hours with 8971 elements.
Creating vector time with 8971 elements.
Creating vector minutes with 8971 elements.
Creating vector time with 8971 elements.
Creating vector seconds with 8971 elements.
Creating vector time with 8971 elements.
Creating vector centiSeconds with 8971 elements.
Creating vector time with 8971 elements.
Creating vector latitude with 8971 elements.
Creating vector time with 8971 elements.
Creating vector longitude with 8971 elements.
Creating vector time with 8971 elements.
Creating vector quality with 8971 elements.
Creating vector time with 8971 elements.
Creating vector numberOfSatellites with 8971 elements.
Creating vector time with 8971 elements.
Creating vector hdop with 8971 elements.
Creating vector time with 8971 elements.
Creating vector antennaHeight with 8971 elements.
Creating vector time with 8971 elements.
Creating vector geoHeight with 8971 elements.
Creating vector time with 8971 elements.
Creating vector dgpsDataAge with 8971 elements.
Creating vector time with 8971 elements.
Creating vector dgpsRSID with 8971 elements.
Creating vector time with 8971 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/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/2017/2017297/2017.297.00/parosci.nc')
Creating vector time with 774777 elements.
Creating vector depth with 774777 elements.
Creating vector time with 774777 elements.
Creating vector temp with 774777 elements.
Creating vector time with 774777 elements.
Creating vector pressure with 774777 elements.
Creating vector time with 774777 elements.
Creating vector temp_period with 774777 elements.
Creating vector time with 774777 elements.
Creating vector pres_period with 774777 elements.
Creating vector time with 774777 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.28108 max(Depth.data) = 202.3844
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.28108 max(Depth.data) = 202.3844
 
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/2017/2017297/2017.297.00/hydroscatlog.nc')
Creating vector time with 313246 elements.
Creating vector Seconds with 313246 elements.
Creating vector time with 313246 elements.
Creating vector HundrethsOfSeconds with 313246 elements.
Creating vector time with 313246 elements.
Creating vector Snorm1 with 313246 elements.
Creating vector time with 313246 elements.
Creating vector Snorm2 with 313246 elements.
Creating vector time with 313246 elements.
Creating vector Snorm3 with 313246 elements.
Creating vector time with 313246 elements.
Creating vector Gain_Status_1 with 313246 elements.
Creating vector time with 313246 elements.
Creating vector Gain_Status_2 with 313246 elements.
Creating vector time with 313246 elements.
Creating vector Gain_Status_3 with 313246 elements.
Creating vector time with 313246 elements.
Creating vector RawDepthValue with 313246 elements.
Creating vector time with 313246 elements.
Creating vector RawTempValue with 313246 elements.
Creating vector time with 313246 elements.
Creating vector Temperature with 313246 elements.
Creating vector time with 313246 elements.
Creating vector ErrorValue with 313246 elements.
Creating vector time with 313246 elements.
Creating vector bb470 with 313246 elements.
Creating vector time with 313246 elements.
Creating vector bb676 with 313246 elements.
Creating vector time with 313246 elements.
Creating vector fl676u with 313246 elements.
Creating vector time with 313246 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/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/2017/2017297/2017.297.00/ctdDriver.nc')
Creating vector time with 313620 elements.
Creating vector conductivity with 313620 elements.
Creating vector time with 313620 elements.
Creating vector temperature with 313620 elements.
Creating vector time with 313620 elements.
Creating vector cond_frequency with 313620 elements.
Creating vector time with 313620 elements.
Creating vector temp_frequency with 313620 elements.
Creating vector time with 313620 elements.
Creating vector spare with 313620 elements.
Creating vector time with 313620 elements.
Creating vector humidity with 313620 elements.
Creating vector time with 313620 elements.
Creating vector flow1 with 313620 elements.
Creating vector time with 313620 elements.
Creating vector CDOM with 313620 elements.
Creating vector time with 313620 elements.
Creating vector dissolvedO2 with 313620 elements.
Creating vector time with 313620 elements.
Creating vector salinity with 313620 elements.
Creating vector time with 313620 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/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/2017/2017297/2017.297.00/ctdDriver2.nc')
Creating vector time with 313572 elements.
Creating vector conductivity with 313572 elements.
Creating vector time with 313572 elements.
Creating vector temperature with 313572 elements.
Creating vector time with 313572 elements.
Creating vector cond_frequency with 313572 elements.
Creating vector time with 313572 elements.
Creating vector temp_frequency with 313572 elements.
Creating vector time with 313572 elements.
Creating vector flow2 with 313572 elements.
Creating vector time with 313572 elements.
Creating vector spare with 313572 elements.
Creating vector time with 313572 elements.
Creating vector salinity with 313572 elements.
Creating vector time with 313572 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/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/2017/2017297/2017.297.00/isuslog.nc')
Creating vector time with 61346 elements.
Creating vector isusNitrate with 61346 elements.
Creating vector time with 61346 elements.
Creating vector isusTemp with 61346 elements.
Creating vector time with 61346 elements.
Creating vector isusQuality with 61346 elements.
Creating vector time with 61346 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/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 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/2017/2017297/2017.297.00/biolume.nc')
Creating vector time with 77559 elements.
Creating vector rrr with 77559 elements.
Creating vector time with 77559 elements.
Creating vector cal_striing with 77559 elements.
Creating vector time with 77559 elements.
Creating vector avg_biolume with 77559 elements.
Creating vector time with 77559 elements.
Creating vector pump with 77559 elements.
Creating vector time with 77559 elements.
Creating vector system_voltage with 77559 elements.
Creating vector time with 77559 elements.
Creating vector flow with 77559 elements.
Creating vector time with 77559 elements.
Creating vector HV with 77559 elements.
Creating vector time with 77559 elements.
Creating vector reserved with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_0 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_1 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_2 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_3 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_4 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_5 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_6 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_7 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_8 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_9 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_10 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_11 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_12 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_13 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_14 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_15 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_16 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_17 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_18 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_19 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_20 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_21 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_22 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_23 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_24 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_25 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_26 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_27 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_28 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_29 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_30 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_31 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_32 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_33 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_34 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_35 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_36 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_37 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_38 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_39 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_40 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_41 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_42 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_43 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_44 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_45 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_46 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_47 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_48 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_49 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_50 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_51 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_52 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_53 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_54 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_55 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_56 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_57 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_58 with 77559 elements.
Creating vector time with 77559 elements.
Creating vector raw_59 with 77559 elements.
Creating vector time with 77559 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/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/2017/2017297/2017.297.00/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (7518 x 994) with 7472892 elements.
Creating vector time with 7518 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (7518 x 994) with 7472892 elements.
Creating vector time with 7518 elements.
Creating vector bin with 994 elements.
Creating matrix countList (7518 x 994) with 7472892 elements.
Creating vector time with 7518 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 7518 elements.
Creating vector time with 7518 elements.
Creating vector transCount with 7518 elements.
Creating vector time with 7518 elements.
Creating vector nonTransCount with 7518 elements.
Creating vector time with 7518 elements.
Creating vector ai_mean with 7518 elements.
Creating vector time with 7518 elements.
Creating vector ai_min with 7518 elements.
Creating vector time with 7518 elements.
Creating vector ai_max with 7518 elements.
Creating vector time with 7518 elements.
Creating vector ai_std with 7518 elements.
Creating vector time with 7518 elements.
Creating vector esd_mean with 7518 elements.
Creating vector time with 7518 elements.
Creating vector esd_min with 7518 elements.
Creating vector time with 7518 elements.
Creating vector esd_max with 7518 elements.
Creating vector time with 7518 elements.
Creating vector esd_std with 7518 elements.
Creating vector time with 7518 elements.
Creating vector countSum with 7518 elements.
Creating vector time with 7518 elements.
Creating vector snapshot with 7518 elements.
Creating vector time with 7518 elements.
Creating vector threshold with 7518 elements.
Creating vector time with 7518 elements.
Creating vector sampleCount with 7518 elements.
Creating vector time with 7518 elements.
Creating vector flowCount with 7518 elements.
Creating vector time with 7518 elements.
Creating vector flowTime with 7518 elements.
Creating vector time with 7518 elements.
Creating vector bufferStatus with 7518 elements.
Creating vector time with 7518 elements.
Creating vector laserLevel with 7518 elements.
Creating vector time with 7518 elements.
Creating vector counter with 7518 elements.
Creating vector time with 7518 elements.
Creating vector counterPeriod with 7518 elements.
Creating vector time with 7518 elements.
Creating vector laserControl with 7518 elements.
Creating vector time with 7518 elements.
Creating vector countUnknownFrameCharacter with 7518 elements.
Creating vector time with 7518 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7518 elements.
Creating vector time with 7518 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7518 elements.
Creating vector time with 7518 elements.
Creating vector flowSpeed with 7518 elements.
Creating vector time with 7518 elements.
Creating vector countShortLFrameError with 7518 elements.
Creating vector time with 7518 elements.
Creating vector countGarbledLFrame with 7518 elements.
Creating vector time with 7518 elements.
Creating vector cFrameEsecs with 7518 elements.
Creating vector time with 7518 elements.
Creating vector correctedSampleCountList with 7518 elements.
Creating vector time with 7518 elements.
Creating vector time with 7518 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017297/2017.297.00/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.297.00.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_2017.297.00.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 25 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/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_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 = 362 Gridding with nix = 1086, iZ = 402
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 380042 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 380042 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 120672 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 10/24/2017 08:30  to 10/25/2017 08:30 

swr =

  145.3739
  291.0603
  450.3846
  570.9950
  618.3789
  618.0447
  556.4913
  390.3135
  257.8835
   89.8054
    5.4099
    0.6460
    1.1144
    1.1772
    1.3314
    1.4061
    1.5865
    1.2397
    0.6781
    0.6738
    1.0865
    1.0011
    0.8521
   26.7147
  156.4513

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2017297_GulperTimes.txt && touch ../results/2017297_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/2017/2017297/2017.297.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2017/2017297/2017.297.00/syslog -startEsecs 1508867136.297 -surveyName Dorado389_2017_297_00_297_00 >> ../results/2017297_GulperTimes.txt
Executing: removeGulpDups.py ../results/2017297_GulperTimes.txt
Bottle: 0 Time: 1508867839.4988 Depth: -0.038808 Dist: 0.70054
Bottle: 1 Time: 1508868361.4931 Depth: 10.0714 Dist: 1.3102
Bottle: 2 Time: 1508868389.8911 Depth: 20.0287 Dist: 1.3445
Bottle: 3 Time: 1508868418.6992 Depth: 30.0095 Dist: 1.3772
Bottle: 4 Time: 1508868448.8971 Depth: 40.0067 Dist: 1.407
Bottle: 5 Time: 1508868502.5034 Depth: 60.0205 Dist: 1.4581
Bottle: 6 Time: 1508868556.2897 Depth: 80.0226 Dist: 1.5217
Bottle: 7 Time: 1508868607.0962 Depth: 100.0036 Dist: 1.5866
Bottle: 8 Time: 1508868672.4918 Depth: 125.3253 Dist: 1.6541
Bottle: 9 Time: 1508868737.7073 Depth: 150.5529 Dist: 1.7327
Bottle: 10 Time: 1508901751.0957 Depth: -0.081415 Dist: 36.0326
Bottle: 11 Time: 1508901816.2913 Depth: 10.0064 Dist: 36.0909
Bottle: 12 Time: 1508901847.6891 Depth: 20.0505 Dist: 36.1281
Bottle: 13 Time: 1508901885.2965 Depth: 30.0199 Dist: 36.1654
Bottle: 14 Time: 1508901922.294 Depth: 40.0501 Dist: 36.202
Bottle: 15 Time: 1508901987.4995 Depth: 60.033 Dist: 36.2851
Bottle: 16 Time: 1508902049.8953 Depth: 80.0948 Dist: 36.3565
Bottle: 17 Time: 1508902115.6907 Depth: 100.0652 Dist: 36.426
Bottle: 18 Time: 1508902268.2903 Depth: 150.0093 Dist: 36.6086
Bottle: 19 Time: 1508902423.2897 Depth: 200.0565 Dist: 36.8001
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_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_2017_297_00_297_00_2column.png
Elapsed time to save image: 10 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_2017_297_00_297_00_biolume.png
Elapsed time to save image: 57 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_2017_297_00_297_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_2017_297_00_297_00_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_2column.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_biolume.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_lopc.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2017/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_2017_297_00_297_00_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2017/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_2017_297_00_297_00_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2017/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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2017/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_2017_297_00_297_00_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2017/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_2017_297_00_297_00_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2017/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_2017_297_00_297_00_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2017/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_2017_297_00_297_00_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2017/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_2017_297_00_297_00_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2017/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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2017_297_00_297_00.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00.kml...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_297_00_297_00_LOPC_Total_Count.kml'
not found.] 
[> In create_data_products (line 419)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 257)] 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00.mat ...
Iterpolating to isus time values...
Interpolating ctd2 temperature...
Interpolating ctd2 salinity...
546 NaNs found in bbpBlue.  Interpolating anyway.
1049 NaNs found in bbpRed.  Interpolating anyway.
90 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 2273 NaN values in array of lon that is 61266 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 58993 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 58993 are not equal to number of Lat lon points = 61266
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_2017_297_00_297_00.txt
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00.txt...
Copied to /mbari/AUVCTD/surveys/2017/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2017/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd2 temperature...
Interpolating ctd2 salinity...
546 NaNs found in bbpBlue.  Interpolating anyway.
1049 NaNs found in bbpRed.  Interpolating anyway.
90 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_2017_297_00_297_00_decim.nc...
Copied to /mbari/AUVCTD/surveys/2017/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_2017_297_00_297_00.nc...
Copied to /mbari/AUVCTD/surveys/2017/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2017/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_297_00_297_00.mat...
Copied to /mbari/AUVCTD/surveys/2017/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to auvctd@listserver.mbari.org ...
!mail -s "Survey Dorado389_2017_297_00_297_00 processed" auvctd@listserver.mbari.org < mail_Dorado389_2017_297_00_297_00.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.297.00.mat
Processing time: 587 seconds