Execution of AUVprocess_main version 1.86 at 2018-05-29T22:53:19Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2008, ['281.03'], '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
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*************************************************************************
Processing AUV mission: 2008.281.03
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/
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/2008/2008281/2008.281.03/navigation.nc')
Creating vector time with 84410 elements.
Creating vector mPos_x with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mPos_y with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mDepth with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mGpsNorth with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mGpsEast with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mGpsValid with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mPhi with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mTheta with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mPsi with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mOmega_x with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mOmega_y with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mOmega_z with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mPsaRange with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mAltitude with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mDvlAltitude with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mWaterSpeed with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mDvlValid with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mDvlNewData with 84410 elements.
Creating vector time with 84410 elements.
Creating vector mDeltaT with 84410 elements.
Creating vector time with 84410 elements.
Creating vector nfix with 84410 elements.
Creating vector time with 84410 elements.
Creating vector efix with 84410 elements.
Creating vector time with 84410 elements.
Creating vector filter_north with 84410 elements.
Creating vector time with 84410 elements.
Creating vector filter_east with 84410 elements.
Creating vector time with 84410 elements.
Creating vector filter_depth with 84410 elements.
Creating vector time with 84410 elements.
Creating vector north_current with 84410 elements.
Creating vector time with 84410 elements.
Creating vector east_current with 84410 elements.
Creating vector time with 84410 elements.
Creating vector speed_bias with 84410 elements.
Creating vector time with 84410 elements.
Creating vector heading_bias with 84410 elements.
Creating vector time with 84410 elements.
Creating vector latitude with 84410 elements.
Creating vector time with 84410 elements.
Creating vector longitude with 84410 elements.
Creating vector time with 84410 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/navigation.nc');
processNav(): median of positive valued depths = 11.801
processNav(): Finding depths less than 82.6068 and times > 0
processNav(): length(Nav.depth) = 84410
processNav(): length(gindx)     = 84384
 
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/2008/2008281/2008.281.03/gps.nc')
Creating vector time with 836 elements.
Creating vector hours with 836 elements.
Creating vector time with 836 elements.
Creating vector minutes with 836 elements.
Creating vector time with 836 elements.
Creating vector seconds with 836 elements.
Creating vector time with 836 elements.
Creating vector centiSeconds with 836 elements.
Creating vector time with 836 elements.
Creating vector latitude with 836 elements.
Creating vector time with 836 elements.
Creating vector longitude with 836 elements.
Creating vector time with 836 elements.
Creating vector quality with 836 elements.
Creating vector time with 836 elements.
Creating vector numberOfSatellites with 836 elements.
Creating vector time with 836 elements.
Creating vector hdop with 836 elements.
Creating vector time with 836 elements.
Creating vector antennaHeight with 836 elements.
Creating vector time with 836 elements.
Creating vector geoHeight with 836 elements.
Creating vector time with 836 elements.
Creating vector dgpsDataAge with 836 elements.
Creating vector time with 836 elements.
Creating vector dgpsRSID with 836 elements.
Creating vector time with 836 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/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/2008/2008281/2008.281.03/parosci.nc')
Creating vector time with 146865 elements.
Creating vector depth with 146865 elements.
Creating vector time with 146865 elements.
Creating vector temp with 146865 elements.
Creating vector time with 146865 elements.
Creating vector pressure with 146865 elements.
Creating vector time with 146865 elements.
Creating vector temp_period with 146865 elements.
Creating vector time with 146865 elements.
Creating vector pres_period with 146865 elements.
Creating vector time with 146865 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -1.961 max(Depth.data) = 752.4158
Found 37 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.91877 max(Depth.data) = 294.3042
 
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/2008/2008281/2008.281.03/hydroscatlog.nc')
Creating vector time with 67597 elements.
Creating vector Seconds with 67597 elements.
Creating vector time with 67597 elements.
Creating vector HundrethsOfSeconds with 67597 elements.
Creating vector time with 67597 elements.
Creating vector Snorm1 with 67597 elements.
Creating vector time with 67597 elements.
Creating vector Snorm2 with 67597 elements.
Creating vector time with 67597 elements.
Creating vector Snorm3 with 67597 elements.
Creating vector time with 67597 elements.
Creating vector Gain_Status_1 with 67597 elements.
Creating vector time with 67597 elements.
Creating vector Gain_Status_2 with 67597 elements.
Creating vector time with 67597 elements.
Creating vector Gain_Status_3 with 67597 elements.
Creating vector time with 67597 elements.
Creating vector RawDepthValue with 67597 elements.
Creating vector time with 67597 elements.
Creating vector RawTempValue with 67597 elements.
Creating vector time with 67597 elements.
Creating vector Temperature with 67597 elements.
Creating vector time with 67597 elements.
Creating vector ErrorValue with 67597 elements.
Creating vector time with 67597 elements.
Creating vector bb470 with 67597 elements.
Creating vector time with 67597 elements.
Creating vector bb676 with 67597 elements.
Creating vector time with 67597 elements.
Creating vector fl676u with 67597 elements.
Creating vector time with 67597 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/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/2008/2008281/2008.281.03/ctdDriver.nc')
Creating vector time with 67463 elements.
Creating vector conductivity with 67463 elements.
Creating vector time with 67463 elements.
Creating vector temperature with 67463 elements.
Creating vector time with 67463 elements.
Creating vector cond_frequency with 67463 elements.
Creating vector time with 67463 elements.
Creating vector temp_frequency with 67463 elements.
Creating vector time with 67463 elements.
Creating vector spare with 67463 elements.
Creating vector time with 67463 elements.
Creating vector humidity with 67463 elements.
Creating vector time with 67463 elements.
Creating vector flow1 with 67463 elements.
Creating vector time with 67463 elements.
Creating vector CDOM with 67463 elements.
Creating vector time with 67463 elements.
Creating vector dissolvedO2 with 67463 elements.
Creating vector time with 67463 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/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/2008/2008281/2008.281.03/ctdDriver2.nc')
Creating vector time with 67462 elements.
Creating vector conductivity with 67462 elements.
Creating vector time with 67462 elements.
Creating vector temperature with 67462 elements.
Creating vector time with 67462 elements.
Creating vector cond_frequency with 67462 elements.
Creating vector time with 67462 elements.
Creating vector temp_frequency with 67462 elements.
Creating vector time with 67462 elements.
Creating vector flow2 with 67462 elements.
Creating vector time with 67462 elements.
Creating vector spare with 67462 elements.
Creating vector time with 67462 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/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/2008/2008281/2008.281.03/isuslog.nc')
Creating vector time with 12349 elements.
Creating vector isusNitrate with 12349 elements.
Creating vector time with 12349 elements.
Creating vector isusTemp with 12349 elements.
Creating vector time with 12349 elements.
Creating vector isusQuality with 12349 elements.
Creating vector time with 12349 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/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/2008/2008281/2008.281.03/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/2008/2008281/2008.281.03/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/2008/2008281/2008.281.03/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/2008/2008281/2008.281.03/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/2008/2008281/2008.281.03/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (532 x 994) with 528808 elements.
Creating vector time with 532 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (532 x 994) with 528808 elements.
Creating vector time with 532 elements.
Creating vector bin with 994 elements.
Creating matrix countList (532 x 994) with 528808 elements.
Creating vector time with 532 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 532 elements.
Creating vector time with 532 elements.
Creating vector transCount with 532 elements.
Creating vector time with 532 elements.
Creating vector nonTransCount with 532 elements.
Creating vector time with 532 elements.
Creating vector ai_mean with 532 elements.
Creating vector time with 532 elements.
Creating vector ai_min with 532 elements.
Creating vector time with 532 elements.
Creating vector ai_max with 532 elements.
Creating vector time with 532 elements.
Creating vector ai_std with 532 elements.
Creating vector time with 532 elements.
Creating vector esd_mean with 532 elements.
Creating vector time with 532 elements.
Creating vector esd_min with 532 elements.
Creating vector time with 532 elements.
Creating vector esd_max with 532 elements.
Creating vector time with 532 elements.
Creating vector esd_std with 532 elements.
Creating vector time with 532 elements.
Creating vector countSum with 532 elements.
Creating vector time with 532 elements.
Creating vector snapshot with 532 elements.
Creating vector time with 532 elements.
Creating vector threshold with 532 elements.
Creating vector time with 532 elements.
Creating vector sampleCount with 532 elements.
Creating vector time with 532 elements.
Creating vector flowCount with 532 elements.
Creating vector time with 532 elements.
Creating vector flowTime with 532 elements.
Creating vector time with 532 elements.
Creating vector bufferStatus with 532 elements.
Creating vector time with 532 elements.
Creating vector laserLevel with 532 elements.
Creating vector time with 532 elements.
Creating vector counter with 532 elements.
Creating vector time with 532 elements.
Creating vector counterPeriod with 532 elements.
Creating vector time with 532 elements.
Creating vector laserControl with 532 elements.
Creating vector time with 532 elements.
Creating vector countUnknownFrameCharacter with 532 elements.
Creating vector time with 532 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 532 elements.
Creating vector time with 532 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 532 elements.
Creating vector time with 532 elements.
Creating vector flowSpeed with 532 elements.
Creating vector time with 532 elements.
Creating vector countShortLFrameError with 532 elements.
Creating vector time with 532 elements.
Creating vector countGarbledLFrame with 532 elements.
Creating vector time with 532 elements.
Creating vector correctedSampleCountList with 532 elements.
Creating vector time with 532 elements.
Creating vector time with 532 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2008/2008281/2008.281.03/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008.281.03.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_2008.281.03.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 10 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03.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 = 300 Gridding with nix = 900, iZ = 49
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...
   bbp470
   bbp676
   fl676_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 = gB470
  cvarname = gB676
  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 78051 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 78051 points from grid Monterey25.grd (2876 x 2447)
Executing: /bin/rm -f ../results/2008281_GulperTimes.txt && touch ../results/2008281_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/2008/2008281/2008.281.03/navigation.nc.ascii?time[0:1:0]
Executing: grep "fired gulper" /mbari/AUVCTD/missionlogs/2008/2008281/2008.281.03/syslog | awk '{print "03."$8, $12}' >> ../results/2008281_GulperTimes.txt
Executing: removeGulpDups.py ../results/2008281_GulperTimes.txt
Bottle: 3 Time: 1223397962.01 Depth: 2.6319 Dist: 7.6318
Bottle: 3.1 Time: 1223399012.22 Depth: 4.6382 Dist: 9.1386
Bottle: 3.2 Time: 1223400104.41 Depth: 4.5701 Dist: 10.7481
Bottle: 3.3 Time: 1223401124.22 Depth: 4.6382 Dist: 12.2119
Bottle: 3.4 Time: 1223402175.61 Depth: 4.7499 Dist: 13.7383
Bottle: 3.5 Time: 1223403203.81 Depth: 3.5635 Dist: 15.1203
Bottle: 3.6 Time: 1223404204.01 Depth: 2.3526 Dist: 16.5456
Bottle: 3.7 Time: 1223405258.01 Depth: 5.0171 Dist: 17.9973
Bottle: 3.8 Time: 1223406322.22 Depth: 3.7758 Dist: 19.4454
Bottle: 3.9 Time: 1223407331.82 Depth: 3.9433 Dist: 20.7064
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_gridded.mat

outvarstr =

    'gF gT gN gS gD gO gB470 gB676 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 gB470
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB676
  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_2008_281_03_281_03_2column.png
Elapsed time to save image: 9 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 gB470
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gB676
  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_2008_281_03_281_03_biolume.png
Elapsed time to save image: 34 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 gB470
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB676
  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_2008_281_03_281_03_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_2008_281_03_281_03_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_2column.png...
Copied to /mbari/AUVCTD/surveys/2008/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_biolume.png...
Copied to /mbari/AUVCTD/surveys/2008/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_lopc.png...
Copied to /mbari/AUVCTD/surveys/2008/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2008/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2008/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2008/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_2008_281_03_281_03_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_Temperature.kmz...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/
cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory
 
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_2008_281_03_281_03_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_Salinity.kmz...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/
cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory
 
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_2008_281_03_281_03_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_Nitrate.kmz...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/
cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory
 
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_2008_281_03_281_03_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_Oxygen.kmz...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/
cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory
 
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @470 nm', jetplus, varlimits(5,:), hs2.bbp470, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_Optical_Backscatter_470_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_Optical_Backscatter_470_nm.kmz...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/
cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory
 
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_Optical_Backscatter_676_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_Optical_Backscatter_676_nm.kmz...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/
cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory
 
KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_Chlorophyll_Fluorescence.kmz...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/
cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory
 
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_2008_281_03_281_03_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_Bioluminescence.kmz...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/
cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory
 
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_2008_281_03_281_03_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2008_281_03_281_03_LOPC_Total_Count.kmz...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/
cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory
 
Creating Dorado389_2008_281_03_281_03.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03.kml...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2008/kml/
cp: failed to access ‘/mbari/AUVCTD/surveys/2008/kml/’: Not a directory
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
1 NaNs found in bbpBlue.  Interpolating anyway.
2 NaNs found in bbpRed.  Interpolating anyway.
Encountered 930 NaN values in array of lon that is 12349 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 11419 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 11419 are not equal to number of Lat lon points = 12349
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_2008_281_03_281_03.txt
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03.txt...
Copied to /mbari/AUVCTD/surveys/2008/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2008/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...
1 NaNs found in bbpBlue.  Interpolating anyway.
2 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_decim.nc...
Copied to /mbari/AUVCTD/surveys/2008/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_2008_281_03_281_03.nc...
Copied to /mbari/AUVCTD/surveys/2008/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2008/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008_281_03_281_03.mat...
Copied to /mbari/AUVCTD/surveys/2008/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2008_281_03_281_03 processed" mccann@mbari.org < mail_Dorado389_2008_281_03_281_03.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2008.281.03.mat
Processing time: 102 seconds