Execution of AUVprocess_main version 1.86 at 2018-05-23T18:29:31Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2010, ['173.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1')
 
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Processing data from SSDS via DODS server
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*************************************************************************
Processing AUV mission: 2010.173.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/
Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Processing DVL navigation data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/navigation.nc')
Creating vector time with 315801 elements.
Creating vector mPos_x with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mPos_y with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mDepth with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mGpsNorth with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mGpsEast with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mGpsValid with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mPhi with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mTheta with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mPsi with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mOmega_x with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mOmega_y with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mOmega_z with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mPsaRange with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mAltitude with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mDvlAltitude with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mWaterSpeed with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mDvlValid with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mDvlNewData with 315801 elements.
Creating vector time with 315801 elements.
Creating vector mDeltaT with 315801 elements.
Creating vector time with 315801 elements.
Creating vector nfix with 315801 elements.
Creating vector time with 315801 elements.
Creating vector efix with 315801 elements.
Creating vector time with 315801 elements.
Creating vector filter_north with 315801 elements.
Creating vector time with 315801 elements.
Creating vector filter_east with 315801 elements.
Creating vector time with 315801 elements.
Creating vector filter_depth with 315801 elements.
Creating vector time with 315801 elements.
Creating vector north_current with 315801 elements.
Creating vector time with 315801 elements.
Creating vector east_current with 315801 elements.
Creating vector time with 315801 elements.
Creating vector speed_bias with 315801 elements.
Creating vector time with 315801 elements.
Creating vector heading_bias with 315801 elements.
Creating vector time with 315801 elements.
Creating vector latitude with 315801 elements.
Creating vector time with 315801 elements.
Creating vector longitude with 315801 elements.
Creating vector time with 315801 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/navigation.nc');
processNav(): median of positive valued depths = 13.411
processNav(): Finding depths less than 93.8768 and times > 0
processNav(): length(Nav.depth) = 315801
processNav(): length(gindx)     = 315801
 
Processing GPS navigation data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/gps.nc')
Creating vector time with 1597 elements.
Creating vector hours with 1597 elements.
Creating vector time with 1597 elements.
Creating vector minutes with 1597 elements.
Creating vector time with 1597 elements.
Creating vector seconds with 1597 elements.
Creating vector time with 1597 elements.
Creating vector centiSeconds with 1597 elements.
Creating vector time with 1597 elements.
Creating vector latitude with 1597 elements.
Creating vector time with 1597 elements.
Creating vector longitude with 1597 elements.
Creating vector time with 1597 elements.
Creating vector quality with 1597 elements.
Creating vector time with 1597 elements.
Creating vector numberOfSatellites with 1597 elements.
Creating vector time with 1597 elements.
Creating vector hdop with 1597 elements.
Creating vector time with 1597 elements.
Creating vector antennaHeight with 1597 elements.
Creating vector time with 1597 elements.
Creating vector geoHeight with 1597 elements.
Creating vector time with 1597 elements.
Creating vector dgpsDataAge with 1597 elements.
Creating vector time with 1597 elements.
Creating vector dgpsRSID with 1597 elements.
Creating vector time with 1597 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/gps.nc');
 
Processing depth data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/parosci.nc')
Creating vector time with 515942 elements.
Creating vector depth with 515942 elements.
Creating vector time with 515942 elements.
Creating vector temp with 515942 elements.
Creating vector time with 515942 elements.
Creating vector pressure with 515942 elements.
Creating vector time with 515942 elements.
Creating vector temp_period with 515942 elements.
Creating vector time with 515942 elements.
Creating vector pres_period with 515942 elements.
Creating vector time with 515942 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.38728 max(Depth.data) = 26.6844
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.38728 max(Depth.data) = 26.6844
 
Processing hs2 backscattering and chlorophyll fluorescence data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/hydroscatlog.nc')
Creating vector time with 70107 elements.
Creating vector Seconds with 70107 elements.
Creating vector time with 70107 elements.
Creating vector HundrethsOfSeconds with 70107 elements.
Creating vector time with 70107 elements.
Creating vector Snorm1 with 70107 elements.
Creating vector time with 70107 elements.
Creating vector Snorm2 with 70107 elements.
Creating vector time with 70107 elements.
Creating vector Snorm3 with 70107 elements.
Creating vector time with 70107 elements.
Creating vector Gain_Status_1 with 70107 elements.
Creating vector time with 70107 elements.
Creating vector Gain_Status_2 with 70107 elements.
Creating vector time with 70107 elements.
Creating vector Gain_Status_3 with 70107 elements.
Creating vector time with 70107 elements.
Creating vector RawDepthValue with 70107 elements.
Creating vector time with 70107 elements.
Creating vector RawTempValue with 70107 elements.
Creating vector time with 70107 elements.
Creating vector Temperature with 70107 elements.
Creating vector time with 70107 elements.
Creating vector ErrorValue with 70107 elements.
Creating vector time with 70107 elements.
Creating vector bb470 with 70107 elements.
Creating vector time with 70107 elements.
Creating vector bb676 with 70107 elements.
Creating vector time with 70107 elements.
Creating vector fl676u with 70107 elements.
Creating vector time with 70107 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/hydroscatlog.nc');
 
Processing CTD #1 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/ctdDriver.nc')
Creating vector time with 252690 elements.
Creating vector conductivity with 252690 elements.
Creating vector time with 252690 elements.
Creating vector temperature with 252690 elements.
Creating vector time with 252690 elements.
Creating vector cond_frequency with 252690 elements.
Creating vector time with 252690 elements.
Creating vector temp_frequency with 252690 elements.
Creating vector time with 252690 elements.
Creating vector spare with 252690 elements.
Creating vector time with 252690 elements.
Creating vector humidity with 252690 elements.
Creating vector time with 252690 elements.
Creating vector flow1 with 252690 elements.
Creating vector time with 252690 elements.
Creating vector CDOM with 252690 elements.
Creating vector time with 252690 elements.
Creating vector dissolvedO2 with 252690 elements.
Creating vector time with 252690 elements.
Creating vector salinity with 252690 elements.
Creating vector time with 252690 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/ctdDriver.cfg
Oxygen calibration loaded from CTD config file (current method)
Using constant flow rate offset for oxygen...
 
Processing CTD #2 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/ctdDriver2.nc')
Creating vector time with 252691 elements.
Creating vector conductivity with 252691 elements.
Creating vector time with 252691 elements.
Creating vector temperature with 252691 elements.
Creating vector time with 252691 elements.
Creating vector cond_frequency with 252691 elements.
Creating vector time with 252691 elements.
Creating vector temp_frequency with 252691 elements.
Creating vector time with 252691 elements.
Creating vector flow2 with 252691 elements.
Creating vector time with 252691 elements.
Creating vector spare with 252691 elements.
Creating vector time with 252691 elements.
Creating vector salinity with 252691 elements.
Creating vector time with 252691 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/ctdDriver2.cfg
 
Processing ISUS data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/isuslog.nc')
Creating vector time with 49054 elements.
Creating vector isusNitrate with 49054 elements.
Creating vector time with 49054 elements.
Creating vector isusTemp with 49054 elements.
Creating vector time with 49054 elements.
Creating vector isusQuality with 49054 elements.
Creating vector time with 49054 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/isuslog.nc');
Total lag applied to nitrate = 6 seconds
 
Processing Biolume data...
[Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 75)
  In processBiolume (line 21)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
[Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 75)
  In processBiolume (line 22)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/biolume.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/2010/2010173/2010.173.00/biolume.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/2010/2010173/2010.173.00/biolume.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/2010/2010173/2010.173.00/biolume.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.


Could not read from biolume.nc returning NaNs for fields.
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (393 x 994) with 390642 elements.
Creating vector time with 393 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (393 x 994) with 390642 elements.
Creating vector time with 393 elements.
Creating vector bin with 994 elements.
Creating matrix countList (393 x 994) with 390642 elements.
Creating vector time with 393 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 393 elements.
Creating vector time with 393 elements.
Creating vector transCount with 393 elements.
Creating vector time with 393 elements.
Creating vector nonTransCount with 393 elements.
Creating vector time with 393 elements.
Creating vector ai_mean with 393 elements.
Creating vector time with 393 elements.
Creating vector ai_min with 393 elements.
Creating vector time with 393 elements.
Creating vector ai_max with 393 elements.
Creating vector time with 393 elements.
Creating vector ai_std with 393 elements.
Creating vector time with 393 elements.
Creating vector esd_mean with 393 elements.
Creating vector time with 393 elements.
Creating vector esd_min with 393 elements.
Creating vector time with 393 elements.
Creating vector esd_max with 393 elements.
Creating vector time with 393 elements.
Creating vector esd_std with 393 elements.
Creating vector time with 393 elements.
Creating vector countSum with 393 elements.
Creating vector time with 393 elements.
Creating vector snapshot with 393 elements.
Creating vector time with 393 elements.
Creating vector threshold with 393 elements.
Creating vector time with 393 elements.
Creating vector sampleCount with 393 elements.
Creating vector time with 393 elements.
Creating vector flowCount with 393 elements.
Creating vector time with 393 elements.
Creating vector flowTime with 393 elements.
Creating vector time with 393 elements.
Creating vector bufferStatus with 393 elements.
Creating vector time with 393 elements.
Creating vector laserLevel with 393 elements.
Creating vector time with 393 elements.
Creating vector counter with 393 elements.
Creating vector time with 393 elements.
Creating vector counterPeriod with 393 elements.
Creating vector time with 393 elements.
Creating vector laserControl with 393 elements.
Creating vector time with 393 elements.
Creating vector countUnknownFrameCharacter with 393 elements.
Creating vector time with 393 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 393 elements.
Creating vector time with 393 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 393 elements.
Creating vector time with 393 elements.
Creating vector flowSpeed with 393 elements.
Creating vector time with 393 elements.
Creating vector countShortLFrameError with 393 elements.
Creating vector time with 393 elements.
Creating vector countGarbledLFrame with 393 elements.
Creating vector time with 393 elements.
Creating vector cFrameEsecs with 393 elements.
Creating vector time with 393 elements.
Creating vector correctedSampleCountList with 393 elements.
Creating vector time with 393 elements.
Creating vector time with 393 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.173.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Calling build_auv_survey.m to construct survey file...

SecondaryDissolvedO2 =

     []

Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.173.00.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 29 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_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 = 850 Gridding with nix = 2550, iZ = 51
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
Only one good point or fewer - NaNing the gBL array.
   BLflow
Only one good point or fewer - NaNing the gBLflow array.
   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
No valid data for gBL
  cvarname = gBLflow
No valid data for gBLflow
  cvarname = gLOPCcount
  cvarname = gLOPCtransCount
  cvarname = gLOPCnonTransCount
  cvarname = gLOPCLCcount
Encountered 0 NaN values in array of lon that is 315478 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 315478 points from grid Monterey25.grd (2876 x 2447)
Executing: /bin/rm -f ../results/2010173_GulperTimes.txt && touch ../results/2010173_GulperTimes.txt
Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010173/2010.173.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010173/2010.173.00/syslog -startEsecs 1277244892.787 -surveyName Dorado389_2010_173_00_173_00 >> ../results/2010173_GulperTimes.txt
Executing: removeGulpDups.py ../results/2010173_GulperTimes.txt
Bottle: 0 Time: 1277304325.1856 Depth: 5.5791 Dist: 78.7256
Bottle: 1 Time: 1277304328 Depth: 5.7908 Dist: 78.7299
Bottle: 2 Time: 1277305081.3838 Depth: 5.7032 Dist: 79.6626
Bottle: 3 Time: 1277305084 Depth: 6.3327 Dist: 79.666
Bottle: 4 Time: 1277305986.5818 Depth: 5.7906 Dist: 80.8218
Bottle: 5 Time: 1277305989 Depth: 6.4154 Dist: 80.8247
Bottle: 6 Time: 1277306942.5863 Depth: 5.7444 Dist: 82.078
Bottle: 7 Time: 1277306945 Depth: 6.1531 Dist: 82.0809
Bottle: 8 Time: 1277307928.7887 Depth: 4.254 Dist: 83.4224
Bottle: 9 Time: 1277307930.9886 Depth: 3.2795 Dist: 83.4244
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_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
2Column contouring gridded variable gT
2Column contouring gridded variable gS
2Column contouring gridded variable gN
2Column contouring gridded variable gO
2Column contouring gridded variable gB420
2Column contouring gridded variable gB700
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_2column.png
Elapsed time to save image: 10 seconds
Biolume contouring gridded variable gD
Biolume contouring gridded variable gT
Biolume contouring gridded variable gS
Biolume contouring gridded variable gN
Biolume contouring gridded variable gO
Biolume contouring gridded variable gB420
Biolume contouring gridded variable gB700
Biolume contouring gridded variable gF
Biolume contouring gridded variable gBL
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_biolume.png
Elapsed time to save image: 43 seconds
2Column contouring gridded variable gLOPCcount
2Column contouring gridded variable gLOPCtransCount
2Column contouring gridded variable gLOPCnonTransCount
2Column contouring gridded variable gLOPCLCcount
2Column contouring gridded variable gT
2Column contouring gridded variable gB420
2Column contouring gridded variable gB700
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_lopc.png
Elapsed time to save image: 8 seconds
 
 
*************************************************************************
Calling plot_survey_stats to produce histogram and profile statistics plots...
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_2column.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_biolume.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_lopc.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing KML files ...
KML = write_kml(survey_shrt_filename_base, 'Temperature', jetplus, varlimits(1,:), ctd1.T, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @420 nm', jetplus, varlimits(5,:), hs2.bbp420, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Optical_Backscatter_420_nm.kml (deflated 92%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @700 nm', jetplus, varlimits(6,:), hs2.bbp700, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2010_173_00_173_00.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00.kml...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_173_00_173_00_LOPC_Total_Count.kml'
not found.] 
[> In create_data_products (line 414)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
7 NaNs found in bbpRed.  Interpolating anyway.
Encountered 50 NaN values in array of lon that is 49054 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 49004 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 49004 are not equal to number of Lat lon points = 49054
AUV track probably goes outside of the range of the .grd file being used.   Setting bottom depths to 1000 m
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00.txt
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00.txt...
Copied to /mbari/AUVCTD/surveys/2010/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2010/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
7 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_decim.nc...
Copied to /mbari/AUVCTD/surveys/2010/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing netCDF file ...
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00.nc...
Copied to /mbari/AUVCTD/surveys/2010/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2010/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_173_00_173_00.mat...
Copied to /mbari/AUVCTD/surveys/2010/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2010_173_00_173_00 processed" mccann@mbari.org < mail_Dorado389_2010_173_00_173_00.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.173.00.mat
Processing time: 467 seconds