Execution of AUVprocess_main version 1.86 at 2018-06-01T20:19:36Z on elvis
Matlab command executed: 
   AUVprocess_main('BIOLUME', 2004, ['254.00'], '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: 2004.254.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/
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/2004/2004254/2004.254.00/navigation.nc')
Creating vector time with 140178 elements.
Creating vector mPos_x with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mPos_y with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mDepth with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mGpsNorth with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mGpsEast with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mGpsValid with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mPhi with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mTheta with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mPsi with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mOmega_x with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mOmega_y with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mOmega_z with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mPsaRange with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mAltitude with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mWaterSpeed with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mDvlValid with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mDvlNewData with 140178 elements.
Creating vector time with 140178 elements.
Creating vector mDeltaT with 140178 elements.
Creating vector time with 140178 elements.
Creating vector latitude with 140178 elements.
Creating vector time with 140178 elements.
Creating vector longitude with 140178 elements.
Creating vector time with 140178 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/navigation.nc');
processNav(): median of positive valued depths = 35.3515
processNav(): Finding depths less than 247.4602 and times > 0
processNav(): length(Nav.depth) = 140178
processNav(): length(gindx)     = 140178
 
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/2004/2004254/2004.254.00/gps.nc')
Creating vector time with 1247 elements.
Creating vector hours with 1247 elements.
Creating vector time with 1247 elements.
Creating vector minutes with 1247 elements.
Creating vector time with 1247 elements.
Creating vector seconds with 1247 elements.
Creating vector time with 1247 elements.
Creating vector centiSeconds with 1247 elements.
Creating vector time with 1247 elements.
Creating vector latitude with 1247 elements.
Creating vector time with 1247 elements.
Creating vector longitude with 1247 elements.
Creating vector time with 1247 elements.
Creating vector quality with 1247 elements.
Creating vector time with 1247 elements.
Creating vector numberOfSatellites with 1247 elements.
Creating vector time with 1247 elements.
Creating vector hdop with 1247 elements.
Creating vector time with 1247 elements.
Creating vector antennaHeight with 1247 elements.
Creating vector time with 1247 elements.
Creating vector geoHeight with 1247 elements.
Creating vector time with 1247 elements.
Creating vector dgpsDataAge with 1247 elements.
Creating vector time with 1247 elements.
Creating vector dgpsRSID with 1247 elements.
Creating vector time with 1247 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/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/2004/2004254/2004.254.00/parosci.nc')
Creating vector time with 140277 elements.
Creating vector depth with 140277 elements.
Creating vector time with 140277 elements.
Creating vector temp with 140277 elements.
Creating vector time with 140277 elements.
Creating vector pressure with 140277 elements.
Creating vector time with 140277 elements.
Creating vector temp_period with 140277 elements.
Creating vector time with 140277 elements.
Creating vector pres_period with 140277 elements.
Creating vector time with 140277 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.081861 max(Depth.data) = 100.9402
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.081861 max(Depth.data) = 100.9402
 
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/2004/2004254/2004.254.00/hydroscatlog.nc')
Creating vector time with 112155 elements.
Creating vector Seconds with 112155 elements.
Creating vector time with 112155 elements.
Creating vector HundrethsOfSeconds with 112155 elements.
Creating vector time with 112155 elements.
Creating vector Snorm1 with 112155 elements.
Creating vector time with 112155 elements.
Creating vector Snorm2 with 112155 elements.
Creating vector time with 112155 elements.
Creating vector Snorm3 with 112155 elements.
Creating vector time with 112155 elements.
Creating vector Gain_Status_1 with 112155 elements.
Creating vector time with 112155 elements.
Creating vector Gain_Status_2 with 112155 elements.
Creating vector time with 112155 elements.
Creating vector Gain_Status_3 with 112155 elements.
Creating vector time with 112155 elements.
Creating vector RawDepthValue with 112155 elements.
Creating vector time with 112155 elements.
Creating vector RawTempValue with 112155 elements.
Creating vector time with 112155 elements.
Creating vector Temperature with 112155 elements.
Creating vector time with 112155 elements.
Creating vector ErrorValue with 112155 elements.
Creating vector time with 112155 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/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/2004/2004254/2004.254.00/ctdDriver.nc')
Creating vector time with 112151 elements.
Creating vector conductivity with 112151 elements.
Creating vector time with 112151 elements.
Creating vector temperature with 112151 elements.
Creating vector time with 112151 elements.
Creating vector cond_frequency with 112151 elements.
Creating vector time with 112151 elements.
Creating vector temp_frequency with 112151 elements.
Creating vector time with 112151 elements.
Creating vector spare with 112151 elements.
Creating vector time with 112151 elements.
Creating vector humidity with 112151 elements.
Creating vector time with 112151 elements.
Creating vector flow1 with 112151 elements.
Creating vector time with 112151 elements.
Creating vector OBS with 112151 elements.
Creating vector time with 112151 elements.
Creating vector dissolvedO2 with 112151 elements.
Creating vector time with 112151 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/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/2004/2004254/2004.254.00/ctdDriver2.nc')
Creating vector time with 112053 elements.
Creating vector conductivity with 112053 elements.
Creating vector time with 112053 elements.
Creating vector temperature with 112053 elements.
Creating vector time with 112053 elements.
Creating vector cond_frequency with 112053 elements.
Creating vector time with 112053 elements.
Creating vector temp_frequency with 112053 elements.
Creating vector time with 112053 elements.
Creating vector flow2 with 112053 elements.
Creating vector time with 112053 elements.
Creating vector spare with 112053 elements.
Creating vector time with 112053 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/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/2004/2004254/2004.254.00/isuslog.nc')
Creating vector time with 17045 elements.
Creating vector isusNitrate with 17045 elements.
Creating vector time with 17045 elements.
Creating vector isusTemp with 17045 elements.
Creating vector time with 17045 elements.
Creating vector isusQuality with 17045 elements.
Creating vector time with 17045 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/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/2004/2004254/2004.254.00/biolume.nc')
Creating vector time with 28060 elements.
Creating vector rrr with 28060 elements.
Creating vector time with 28060 elements.
Creating vector cal_striing with 28060 elements.
Creating vector time with 28060 elements.
Creating vector pump with 28060 elements.
Creating vector time with 28060 elements.
Creating vector flow with 28060 elements.
Creating vector time with 28060 elements.
Creating vector humidity with 28060 elements.
Creating vector time with 28060 elements.
Creating vector temperature with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_0 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_1 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_2 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_3 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_4 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_5 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_6 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_7 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_8 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_9 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_10 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_11 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_12 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_13 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_14 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_15 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_16 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_17 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_18 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_19 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_20 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_21 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_22 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_23 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_24 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_25 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_26 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_27 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_28 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_29 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_30 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_31 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_32 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_33 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_34 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_35 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_36 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_37 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_38 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_39 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_40 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_41 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_42 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_43 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_44 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_45 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_46 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_47 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_48 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_49 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_50 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_51 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_52 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_53 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_54 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_55 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_56 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_57 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_58 with 28060 elements.
Creating vector time with 28060 elements.
Creating vector raw_59 with 28060 elements.
Creating vector time with 28060 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004254/2004.254.00/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/2004/2004254/2004.254.00/lopc.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/2004/2004254/2004.254.00/lopc.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/2004/2004254/2004.254.00/lopc.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/2004/2004254/2004.254.00/lopc.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


*** Setting lopc structure to NaNs. *** 
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.254.00.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_2004.254.00.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 13 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_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 = 132 Gridding with nix = 396, iZ = 199
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
   BLflow
   LOPC
Only one good point or fewer - NaNing the gLOPCcount array.
                             - NaNing the gLOPCtransCount array.
                             - NaNing the gLOPCnonTransCount array.
                             - NaNing the gLOPCLCcount array.
 
Masking and filtering with median filter of size 5...
  cvarname = gT
  cvarname = gS
  cvarname = gO
  cvarname = gN
  cvarname = gF
  cvarname = gB470
  cvarname = gB676
  cvarname = gBL
  cvarname = gBLflow
  cvarname = gLOPCcount
No valid data for gLOPCcount
  cvarname = gLOPCtransCount
No valid data for gLOPCtransCount
  cvarname = gLOPCnonTransCount
No valid data for gLOPCnonTransCount
  cvarname = gLOPCLCcount
No valid data for gLOPCLCcount
Encountered 0 NaN values in array of lon that is 138905 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 138905 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 119090 elements.
*** Could not find start or end index in Met data read from http://elvis.shore.mbari.org/thredds/dodsC/agg/OS_MBARI-M1_R_M
Looking for start days = 19976.1151 since 1/1/1950
Looking for end   days = 19976.4396
sIndx = 
eIndx = 
Met data goes from 20017.6042 to 24988.8125
No SWR data loaded from URL.
Executing: /bin/rm -f ../results/2004254_GulperTimes.txt && touch ../results/2004254_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/2004/2004254/2004.254.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004254/2004.254.00/syslog -startEsecs 1094784341.995 -surveyName Dorado389_2004_254_00_254_00 >> ../results/2004254_GulperTimes.txt
Executing: removeGulpDups.py ../results/2004254_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_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
Did not add swr plot to the image.
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_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 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
SWR image not added to the plot.
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_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
Did not add swr plot to the image.
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_lopc.png
Elapsed time to save image: 10 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_2004_254_00_254_00_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_2column.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_biolume.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_lopc.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2004/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_2004_254_00_254_00_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2004/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_2004_254_00_254_00_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2004/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_2004_254_00_254_00_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2004/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_2004_254_00_254_00_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
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_2004_254_00_254_00_Optical_Backscatter_470_nm.kml (deflated 92%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_Optical_Backscatter_470_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
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_2004_254_00_254_00_Optical_Backscatter_676_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_Optical_Backscatter_676_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2004/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.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2004/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);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_Bioluminescence.kml (deflated 92%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2004/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);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_00_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2004_254_00_254_00.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00.kml...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_254_00_254_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_2004_254_00_254_00.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
1 NaNs found in bbpBlue.  Interpolating anyway.
1 NaNs found in bbpRed.  Interpolating anyway.
Encountered 152 NaN values in array of lon that is 17045 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 16893 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 16893 are not equal to number of Lat lon points = 17045
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_2004_254_00_254_00.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00.txt...
Copied to /mbari/AUVCTD/surveys/2004/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_Gulper.txt...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2004/odv/
cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
1 NaNs found in bbpBlue.  Interpolating anyway.
1 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_decim.nc...
Copied to /mbari/AUVCTD/surveys/2004/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_2004_254_00_254_00.nc...
Copied to /mbari/AUVCTD/surveys/2004/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2004/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_254_00_254_00.mat...
Copied to /mbari/AUVCTD/surveys/2004/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2004_254_00_254_00 processed" mccann@mbari.org < mail_Dorado389_2004_254_00_254_00.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.254.00.mat
Processing time: 218 seconds