Execution of AUVprocess_main version 1.86 at 2018-06-02T16:20:22Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2012, ['256.00'], '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: 2012.256.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/
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/2012/2012256/2012.256.00/navigation.nc')
Creating vector time with 78118 elements.
Creating vector mPos_x with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mPos_y with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mDepth with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mGpsNorth with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mGpsEast with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mGpsValid with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mPhi with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mTheta with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mPsi with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mOmega_x with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mOmega_y with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mOmega_z with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mPsaRange with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mAltitude with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mDvlAltitude with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mEchoAltitude with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mEchoHorizRange with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mEchoAltitudeLast with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mEchoHorizRangeLast with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mEchoNumOfPings with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mWaterSpeed with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mDvlValid with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mDvlNewData with 78118 elements.
Creating vector time with 78118 elements.
Creating vector mDeltaT with 78118 elements.
Creating vector time with 78118 elements.
Creating vector nfix with 78118 elements.
Creating vector time with 78118 elements.
Creating vector efix with 78118 elements.
Creating vector time with 78118 elements.
Creating vector filter_north with 78118 elements.
Creating vector time with 78118 elements.
Creating vector filter_east with 78118 elements.
Creating vector time with 78118 elements.
Creating vector filter_depth with 78118 elements.
Creating vector time with 78118 elements.
Creating vector north_current with 78118 elements.
Creating vector time with 78118 elements.
Creating vector east_current with 78118 elements.
Creating vector time with 78118 elements.
Creating vector speed_bias with 78118 elements.
Creating vector time with 78118 elements.
Creating vector heading_bias with 78118 elements.
Creating vector time with 78118 elements.
Creating vector latitude with 78118 elements.
Creating vector time with 78118 elements.
Creating vector longitude with 78118 elements.
Creating vector time with 78118 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/navigation.nc');
[Warning: P-file /mbari/matlab/toolbox/matlab/strfun/num2str.p is older than
MATLAB file /mbari/matlab/toolbox/matlab/strfun/num2str.m.
/mbari/matlab/toolbox/matlab/strfun/num2str.p may be obsolete and may need to
be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In processNav (line 62)
  In processAUVmission (line 60)
  In AUVprocess_main (line 225)] 
processNav(): median of positive valued depths = 65.8425
processNav(): Finding depths less than 460.8976 and times > 0
processNav(): length(Nav.depth) = 78118
processNav(): length(gindx)     = 78118
 
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/2012/2012256/2012.256.00/gps.nc')
Creating vector time with 872 elements.
Creating vector hours with 872 elements.
Creating vector time with 872 elements.
Creating vector minutes with 872 elements.
Creating vector time with 872 elements.
Creating vector seconds with 872 elements.
Creating vector time with 872 elements.
Creating vector centiSeconds with 872 elements.
Creating vector time with 872 elements.
Creating vector latitude with 872 elements.
Creating vector time with 872 elements.
Creating vector longitude with 872 elements.
Creating vector time with 872 elements.
Creating vector quality with 872 elements.
Creating vector time with 872 elements.
Creating vector numberOfSatellites with 872 elements.
Creating vector time with 872 elements.
Creating vector hdop with 872 elements.
Creating vector time with 872 elements.
Creating vector antennaHeight with 872 elements.
Creating vector time with 872 elements.
Creating vector geoHeight with 872 elements.
Creating vector time with 872 elements.
Creating vector dgpsDataAge with 872 elements.
Creating vector time with 872 elements.
Creating vector dgpsRSID with 872 elements.
Creating vector time with 872 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/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/2012/2012256/2012.256.00/parosci.nc')
Creating vector time with 132810 elements.
Creating vector depth with 132810 elements.
Creating vector time with 132810 elements.
Creating vector temp with 132810 elements.
Creating vector time with 132810 elements.
Creating vector pressure with 132810 elements.
Creating vector time with 132810 elements.
Creating vector temp_period with 132810 elements.
Creating vector time with 132810 elements.
Creating vector pres_period with 132810 elements.
Creating vector time with 132810 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.28804 max(Depth.data) = 152.0001
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.28804 max(Depth.data) = 152.0001
[Warning: P-file /mbari/matlab/toolbox/matlab/ops/unique.p is older than MATLAB
file /mbari/matlab/toolbox/matlab/ops/unique.m.
/mbari/matlab/toolbox/matlab/ops/unique.p may be obsolete and may need to be
regenerated.
Type "help pcode" for information about generating P-files.] 
[> In fix_depth_time (line 6)
  In processDepth (line 65)
  In processAUVmission (line 106)
  In AUVprocess_main (line 225)] 
 
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/2012/2012256/2012.256.00/hydroscatlog.nc')
Creating vector time with 62588 elements.
Creating vector Seconds with 62588 elements.
Creating vector time with 62588 elements.
Creating vector HundrethsOfSeconds with 62588 elements.
Creating vector time with 62588 elements.
Creating vector Snorm1 with 62588 elements.
Creating vector time with 62588 elements.
Creating vector Snorm2 with 62588 elements.
Creating vector time with 62588 elements.
Creating vector Snorm3 with 62588 elements.
Creating vector time with 62588 elements.
Creating vector Gain_Status_1 with 62588 elements.
Creating vector time with 62588 elements.
Creating vector Gain_Status_2 with 62588 elements.
Creating vector time with 62588 elements.
Creating vector Gain_Status_3 with 62588 elements.
Creating vector time with 62588 elements.
Creating vector RawDepthValue with 62588 elements.
Creating vector time with 62588 elements.
Creating vector RawTempValue with 62588 elements.
Creating vector time with 62588 elements.
Creating vector Temperature with 62588 elements.
Creating vector time with 62588 elements.
Creating vector ErrorValue with 62588 elements.
Creating vector time with 62588 elements.
Creating vector bb470 with 62588 elements.
Creating vector time with 62588 elements.
Creating vector bb676 with 62588 elements.
Creating vector time with 62588 elements.
Creating vector fl676u with 62588 elements.
Creating vector time with 62588 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/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/2012/2012256/2012.256.00/ctdDriver.nc')
Creating vector time with 62468 elements.
Creating vector conductivity with 62468 elements.
Creating vector time with 62468 elements.
Creating vector temperature with 62468 elements.
Creating vector time with 62468 elements.
Creating vector cond_frequency with 62468 elements.
Creating vector time with 62468 elements.
Creating vector temp_frequency with 62468 elements.
Creating vector time with 62468 elements.
Creating vector spare with 62468 elements.
Creating vector time with 62468 elements.
Creating vector humidity with 62468 elements.
Creating vector time with 62468 elements.
Creating vector flow1 with 62468 elements.
Creating vector time with 62468 elements.
Creating vector CDOM with 62468 elements.
Creating vector time with 62468 elements.
Creating vector dissolvedO2 with 62468 elements.
Creating vector time with 62468 elements.
Creating vector salinity with 62468 elements.
Creating vector time with 62468 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/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/2012/2012256/2012.256.00/ctdDriver2.nc')
Creating vector time with 62532 elements.
Creating vector conductivity with 62532 elements.
Creating vector time with 62532 elements.
Creating vector temperature with 62532 elements.
Creating vector time with 62532 elements.
Creating vector cond_frequency with 62532 elements.
Creating vector time with 62532 elements.
Creating vector temp_frequency with 62532 elements.
Creating vector time with 62532 elements.
Creating vector flow2 with 62532 elements.
Creating vector time with 62532 elements.
Creating vector spare with 62532 elements.
Creating vector time with 62532 elements.
Creating vector salinity with 62532 elements.
Creating vector time with 62532 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/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/2012/2012256/2012.256.00/isuslog.nc')
Creating vector time with 12289 elements.
Creating vector isusNitrate with 12289 elements.
Creating vector time with 12289 elements.
Creating vector isusTemp with 12289 elements.
Creating vector time with 12289 elements.
Creating vector isusQuality with 12289 elements.
Creating vector time with 12289 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/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/2012/2012256/2012.256.00/biolume.nc')
Creating vector time with 15398 elements.
Creating vector rrr with 15398 elements.
Creating vector time with 15398 elements.
Creating vector cal_striing with 15398 elements.
Creating vector time with 15398 elements.
Creating vector avg_biolume with 15398 elements.
Creating vector time with 15398 elements.
Creating vector pump with 15398 elements.
Creating vector time with 15398 elements.
Creating vector system_voltage with 15398 elements.
Creating vector time with 15398 elements.
Creating vector flow with 15398 elements.
Creating vector time with 15398 elements.
Creating vector HV with 15398 elements.
Creating vector time with 15398 elements.
Creating vector reserved with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_0 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_1 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_2 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_3 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_4 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_5 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_6 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_7 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_8 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_9 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_10 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_11 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_12 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_13 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_14 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_15 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_16 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_17 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_18 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_19 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_20 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_21 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_22 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_23 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_24 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_25 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_26 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_27 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_28 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_29 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_30 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_31 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_32 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_33 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_34 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_35 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_36 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_37 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_38 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_39 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_40 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_41 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_42 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_43 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_44 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_45 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_46 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_47 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_48 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_49 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_50 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_51 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_52 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_53 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_54 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_55 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_56 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_57 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_58 with 15398 elements.
Creating vector time with 15398 elements.
Creating vector raw_59 with 15398 elements.
Creating vector time with 15398 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2012/2012256/2012.256.00/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/2012/2012256/2012.256.00/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/2012/2012256/2012.256.00/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/2012/2012256/2012.256.00/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/2012/2012256/2012.256.00/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_2012.256.00.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_2012.256.00.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 3 segments.
[Warning: MATLAB has disabled some advanced graphics rendering features by
switching to software OpenGL. For more information, click <a
href="matlab:opengl('problems')">here</a>.] 
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_00_nav_adjust.png
[Warning: P-file /mbari/matlab/toolbox/matlab/imagesci/imformats.p is older than
MATLAB file /mbari/matlab/toolbox/matlab/imagesci/imformats.m.
/mbari/matlab/toolbox/matlab/imagesci/imformats.p may be obsolete and may need
to be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In imwrite>parse_inputs (line 557)
  In imwrite (line 418)
  In writeRaster
  In printingGenerateOutput
  In alternatePrintPath
  In print (line 82)
  In create_data_products (line 99)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
[Warning: P-file /mbari/matlab/toolbox/matlab/timefun/datevec.p is older than
MATLAB file /mbari/matlab/toolbox/matlab/timefun/datevec.m.
/mbari/matlab/toolbox/matlab/timefun/datevec.p may be obsolete and may need to
be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In datenum (line 103)
  In writepng (line 232)
  In imwrite (line 485)
  In writeRaster
  In printingGenerateOutput
  In alternatePrintPath
  In print (line 82)
  In create_data_products (line 99)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_00.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_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 = 44 Gridding with nix = 132, iZ = 301
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 77802 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: Some input points were outside the grid domain(s).
grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447)
No depth array returned by grdtrack.  Perhaps grdtrack could not be found in the search path.
Setting ocean depths to 4000m for the track.
Getting short wave radiation data from M1 for little plot above the biolume section plot
Creating vector TIME with 119110 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 09/11/2012 17:30  to 09/11/2012 23:30 

swr =

   NaN
   NaN
   NaN
   NaN
   NaN
   NaN
   NaN

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_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/2012256_GulperTimes.txt && touch ../results/2012256_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/2012/2012256/2012.256.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2012/2012256/2012.256.00/syslog -startEsecs 1347416556.9806 -surveyName Dorado389_2012_256_00_256_00 >> ../results/2012256_GulperTimes.txt
Cannot open /mbari/AUVCTD/missionlogs/2012/2012256/2012.256.00/syslog: No such file or directory
Executing: removeGulpDups.py ../results/2012256_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_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_256_00_256_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_256_00_256_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_256_00_256_00_lopc.png
Elapsed time to save image: 5 seconds
 
 
*************************************************************************
Calling plot_survey_stats to produce histogram and profile statistics plots...
[Warning: P-file /mbari/matlab/toolbox/matlab/graph2d/subplot.p is older than
MATLAB file /mbari/matlab/toolbox/matlab/graph2d/subplot.m.
/mbari/matlab/toolbox/matlab/graph2d/subplot.p may be obsolete and may need to
be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In plot_survey_stats (line 47)
  In create_data_products (line 128)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_00_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_00_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_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_256_00_256_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_256_00_256_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_256_00_256_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_256_00_256_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_256_00_256_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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_00_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_00_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_00_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_00_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_00_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_00_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_00_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_00_Bioluminescence.kml (deflated 92%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_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.
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_00_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2012_256_00_256_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_256_00_256_00.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_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_256_00_256_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_256_00_256_00.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
4 NaNs found in bbpBlue.  Interpolating anyway.
7 NaNs found in bbpRed.  Interpolating anyway.
Encountered 49 NaN values in array of lon that is 12288 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: Some input points were outside the grid domain(s).
grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447)
No depth array returned by grdtrack.  Setting bottom depth to 1000 m
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_00.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_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_256_00_256_00_Gulper.txt...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2012/odv/
cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_00_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
4 NaNs found in bbpBlue.  Interpolating anyway.
7 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012_256_00_256_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_256_00_256_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_256_00_256_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_256_00_256_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_256_00_256_00 processed" mccann@mbari.org < mail_Dorado389_2012_256_00_256_00.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2012.256.00.mat
Processing time: 109 seconds