Execution of AUVprocess_main version 1.86 at 2018-05-24T15:52:26Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2012, ['269.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1')
 
*************************************************************************
Processing data from SSDS via DODS server
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2012.269.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/
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/2012/2012269/2012.269.00/navigation.nc')
Creating vector time with 91185 elements.
Creating vector mPos_x with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mPos_y with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mDepth with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mGpsNorth with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mGpsEast with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mGpsValid with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mPhi with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mTheta with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mPsi with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mOmega_x with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mOmega_y with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mOmega_z with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mPsaRange with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mAltitude with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mDvlAltitude with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mEchoAltitude with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mEchoHorizRange with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mEchoAltitudeLast with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mEchoHorizRangeLast with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mEchoNumOfPings with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mWaterSpeed with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mDvlValid with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mDvlNewData with 91185 elements.
Creating vector time with 91185 elements.
Creating vector mDeltaT with 91185 elements.
Creating vector time with 91185 elements.
Creating vector nfix with 91185 elements.
Creating vector time with 91185 elements.
Creating vector efix with 91185 elements.
Creating vector time with 91185 elements.
Creating vector filter_north with 91185 elements.
Creating vector time with 91185 elements.
Creating vector filter_east with 91185 elements.
Creating vector time with 91185 elements.
Creating vector filter_depth with 91185 elements.
Creating vector time with 91185 elements.
Creating vector north_current with 91185 elements.
Creating vector time with 91185 elements.
Creating vector east_current with 91185 elements.
Creating vector time with 91185 elements.
Creating vector speed_bias with 91185 elements.
Creating vector time with 91185 elements.
Creating vector heading_bias with 91185 elements.
Creating vector time with 91185 elements.
Creating vector latitude with 91185 elements.
Creating vector time with 91185 elements.
Creating vector longitude with 91185 elements.
Creating vector time with 91185 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/navigation.nc');
processNav(): median of positive valued depths = 11.965
processNav(): Finding depths less than 83.7552 and times > 0
processNav(): length(Nav.depth) = 91185
processNav(): length(gindx)     = 91185
 
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/2012/2012269/2012.269.00/gps.nc')
Creating vector time with 4050 elements.
Creating vector hours with 4050 elements.
Creating vector time with 4050 elements.
Creating vector minutes with 4050 elements.
Creating vector time with 4050 elements.
Creating vector seconds with 4050 elements.
Creating vector time with 4050 elements.
Creating vector centiSeconds with 4050 elements.
Creating vector time with 4050 elements.
Creating vector latitude with 4050 elements.
Creating vector time with 4050 elements.
Creating vector longitude with 4050 elements.
Creating vector time with 4050 elements.
Creating vector quality with 4050 elements.
Creating vector time with 4050 elements.
Creating vector numberOfSatellites with 4050 elements.
Creating vector time with 4050 elements.
Creating vector hdop with 4050 elements.
Creating vector time with 4050 elements.
Creating vector antennaHeight with 4050 elements.
Creating vector time with 4050 elements.
Creating vector geoHeight with 4050 elements.
Creating vector time with 4050 elements.
Creating vector dgpsDataAge with 4050 elements.
Creating vector time with 4050 elements.
Creating vector dgpsRSID with 4050 elements.
Creating vector time with 4050 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/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/2012/2012269/2012.269.00/parosci.nc')
Creating vector time with 154758 elements.
Creating vector depth with 154758 elements.
Creating vector time with 154758 elements.
Creating vector temp with 154758 elements.
Creating vector time with 154758 elements.
Creating vector pressure with 154758 elements.
Creating vector time with 154758 elements.
Creating vector temp_period with 154758 elements.
Creating vector time with 154758 elements.
Creating vector pres_period with 154758 elements.
Creating vector time with 154758 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.24454 max(Depth.data) = 20.7817
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.24454 max(Depth.data) = 20.7817
 
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/2012/2012269/2012.269.00/hydroscatlog.nc')
Creating vector time with 73039 elements.
Creating vector Seconds with 73039 elements.
Creating vector time with 73039 elements.
Creating vector HundrethsOfSeconds with 73039 elements.
Creating vector time with 73039 elements.
Creating vector Snorm1 with 73039 elements.
Creating vector time with 73039 elements.
Creating vector Snorm2 with 73039 elements.
Creating vector time with 73039 elements.
Creating vector Snorm3 with 73039 elements.
Creating vector time with 73039 elements.
Creating vector Gain_Status_1 with 73039 elements.
Creating vector time with 73039 elements.
Creating vector Gain_Status_2 with 73039 elements.
Creating vector time with 73039 elements.
Creating vector Gain_Status_3 with 73039 elements.
Creating vector time with 73039 elements.
Creating vector RawDepthValue with 73039 elements.
Creating vector time with 73039 elements.
Creating vector RawTempValue with 73039 elements.
Creating vector time with 73039 elements.
Creating vector Temperature with 73039 elements.
Creating vector time with 73039 elements.
Creating vector ErrorValue with 73039 elements.
Creating vector time with 73039 elements.
Creating vector bb470 with 73039 elements.
Creating vector time with 73039 elements.
Creating vector bb676 with 73039 elements.
Creating vector time with 73039 elements.
Creating vector fl676u with 73039 elements.
Creating vector time with 73039 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/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/2012/2012269/2012.269.00/ctdDriver.nc')
Creating vector time with 72925 elements.
Creating vector conductivity with 72925 elements.
Creating vector time with 72925 elements.
Creating vector temperature with 72925 elements.
Creating vector time with 72925 elements.
Creating vector cond_frequency with 72925 elements.
Creating vector time with 72925 elements.
Creating vector temp_frequency with 72925 elements.
Creating vector time with 72925 elements.
Creating vector spare with 72925 elements.
Creating vector time with 72925 elements.
Creating vector humidity with 72925 elements.
Creating vector time with 72925 elements.
Creating vector flow1 with 72925 elements.
Creating vector time with 72925 elements.
Creating vector CDOM with 72925 elements.
Creating vector time with 72925 elements.
Creating vector dissolvedO2 with 72925 elements.
Creating vector time with 72925 elements.
Creating vector salinity with 72925 elements.
Creating vector time with 72925 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/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/2012/2012269/2012.269.00/ctdDriver2.nc')
Creating vector time with 72952 elements.
Creating vector conductivity with 72952 elements.
Creating vector time with 72952 elements.
Creating vector temperature with 72952 elements.
Creating vector time with 72952 elements.
Creating vector cond_frequency with 72952 elements.
Creating vector time with 72952 elements.
Creating vector temp_frequency with 72952 elements.
Creating vector time with 72952 elements.
Creating vector flow2 with 72952 elements.
Creating vector time with 72952 elements.
Creating vector spare with 72952 elements.
Creating vector time with 72952 elements.
Creating vector salinity with 72952 elements.
Creating vector time with 72952 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/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/2012/2012269/2012.269.00/isuslog.nc')
Creating vector time with 16904 elements.
Creating vector isusNitrate with 16904 elements.
Creating vector time with 16904 elements.
Creating vector isusTemp with 16904 elements.
Creating vector time with 16904 elements.
Creating vector isusQuality with 16904 elements.
Creating vector time with 16904 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/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/2012/2012269/2012.269.00/biolume.nc')
Creating vector time with 17968 elements.
Creating vector rrr with 17968 elements.
Creating vector time with 17968 elements.
Creating vector cal_striing with 17968 elements.
Creating vector time with 17968 elements.
Creating vector avg_biolume with 17968 elements.
Creating vector time with 17968 elements.
Creating vector pump with 17968 elements.
Creating vector time with 17968 elements.
Creating vector system_voltage with 17968 elements.
Creating vector time with 17968 elements.
Creating vector flow with 17968 elements.
Creating vector time with 17968 elements.
Creating vector HV with 17968 elements.
Creating vector time with 17968 elements.
Creating vector reserved with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_0 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_1 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_2 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_3 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_4 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_5 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_6 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_7 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_8 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_9 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_10 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_11 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_12 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_13 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_14 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_15 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_16 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_17 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_18 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_19 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_20 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_21 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_22 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_23 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_24 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_25 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_26 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_27 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_28 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_29 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_30 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_31 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_32 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_33 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_34 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_35 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_36 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_37 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_38 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_39 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_40 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_41 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_42 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_43 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_44 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_45 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_46 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_47 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_48 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_49 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_50 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_51 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_52 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_53 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_54 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_55 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_56 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_57 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_58 with 17968 elements.
Creating vector time with 17968 elements.
Creating vector raw_59 with 17968 elements.
Creating vector time with 17968 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012269/2012.269.00/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/2012/2012269/2012.269.00/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/2012/2012269/2012.269.00/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/2012/2012269/2012.269.00/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/2012/2012269/2012.269.00/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_2012.269.00.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_2012.269.00.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 9 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_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 = 180 Gridding with nix = 540, iZ = 38
Using mean boxcar filter of vector...
Using mean boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Gridding...
   T
   S
   O
Using median boxcar filter of vector...
Using median boxcar filter of vector...
Using median boxcar filter of vector...
   bbp420
   bbp700
   fl700_uncorr
   N
   BL
   BLflow
   LOPC
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 = gB420
  cvarname = gB700
  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 89101 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 89101 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 118894 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 09/25/2012 07:29  to 09/25/2012 14:30 

swr =

   NaN
   NaN
   NaN
   NaN
   NaN
   NaN
   NaN
   NaN

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_swr.png
[Warning: Contour not rendered for non-finite ZData] 
[> In contourf (line 60)
  In plot_sections (line 564)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
Done plotting SWR.
Executing: /bin/rm -f ../results/2012269_GulperTimes.txt && touch ../results/2012269_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/2012/2012269/2012.269.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2012/2012269/2012.269.00/syslog -startEsecs 1348590969.8175 -surveyName Dorado389_2012_269_00_269_00 >> ../results/2012269_GulperTimes.txt
Executing: removeGulpDups.py ../results/2012269_GulperTimes.txt
Bottle: 0 Time: 1348591550 Depth: 11.8545 Dist: 0.29567
Bottle: 1 Time: 1348592357 Depth: 16.7154 Dist: 1.6753
Bottle: 2 Time: 1348593033 Depth: 9.2535 Dist: 2.2581
Bottle: 3 Time: 1348594833 Depth: 9.9007 Dist: 4.4871
Bottle: 4 Time: 1348595874 Depth: 16.1575 Dist: 5.7065
Bottle: 5 Time: 1348597793 Depth: 1.3601 Dist: 6.9081
Bottle: 6 Time: 1348599473 Depth: 18.1771 Dist: 9.2168
Bottle: 7 Time: 1348601132 Depth: 20.016 Dist: 10.9689
Bottle: 8 Time: 1348602384 Depth: 18.4904 Dist: 12.3645
Bottle: 9 Time: 1348603043 Depth: 20.1822 Dist: 13.2079
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_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_2012_269_00_269_00_2column.png
Elapsed time to save image: 5 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_2012_269_00_269_00_biolume.png
Elapsed time to save image: 26 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_2012_269_00_269_00_lopc.png
Elapsed time to save image: 5 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_2012_269_00_269_00_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_2column.png...
Copied to /mbari/AUVCTD/surveys/2012/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_biolume.png...
Copied to /mbari/AUVCTD/surveys/2012/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_lopc.png...
Copied to /mbari/AUVCTD/surveys/2012/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2012/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2012/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2012/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_2012_269_00_269_00_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_269_00_269_00_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2012/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_2012_269_00_269_00_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_269_00_269_00_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2012/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_2012_269_00_269_00_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_269_00_269_00_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2012/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_2012_269_00_269_00_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_269_00_269_00_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2012/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_2012_269_00_269_00_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_269_00_269_00_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2012/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_2012_269_00_269_00_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_269_00_269_00_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2012/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_2012_269_00_269_00_Chlorophyll_Fluorescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_269_00_269_00_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2012/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_2012_269_00_269_00_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_269_00_269_00_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2012/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_2012_269_00_269_00_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_269_00_269_00_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2012/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2012_269_00_269_00.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00.kml...
Copied to /mbari/AUVCTD/surveys/2012/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_269_00_269_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_2012_269_00_269_00.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
6 NaNs found in bbpBlue.  Interpolating anyway.
9 NaNs found in bbpRed.  Interpolating anyway.
12 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 375 NaN values in array of lon that is 16626 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 16251 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 16251 are not equal to number of Lat lon points = 16626
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_2012_269_00_269_00.txt
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00.txt...
Copied to /mbari/AUVCTD/surveys/2012/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2012/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...
6 NaNs found in bbpBlue.  Interpolating anyway.
9 NaNs found in bbpRed.  Interpolating anyway.
12 NaNs found in flRed_uncorr.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_decim.nc...
Copied to /mbari/AUVCTD/surveys/2012/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_2012_269_00_269_00.nc...
Copied to /mbari/AUVCTD/surveys/2012/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2012/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_269_00_269_00.mat...
Copied to /mbari/AUVCTD/surveys/2012/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2012_269_00_269_00 processed" mccann@mbari.org < mail_Dorado389_2012_269_00_269_00.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012.269.00.mat
Processing time: 114 seconds