Execution of AUVprocess_main version 1.86 at 2018-05-29T19:12:23Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2009, ['111.01'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd2')
 
*************************************************************************
Processing data from SSDS via DODS server
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2009.111.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/
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/2009/2009111/2009.111.01/navigation.nc')
Creating vector time with 347874 elements.
Creating vector mPos_x with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mPos_y with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mDepth with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mGpsNorth with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mGpsEast with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mGpsValid with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mPhi with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mTheta with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mPsi with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mOmega_x with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mOmega_y with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mOmega_z with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mPsaRange with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mAltitude with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mDvlAltitude with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mWaterSpeed with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mDvlValid with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mDvlNewData with 347874 elements.
Creating vector time with 347874 elements.
Creating vector mDeltaT with 347874 elements.
Creating vector time with 347874 elements.
Creating vector nfix with 347874 elements.
Creating vector time with 347874 elements.
Creating vector efix with 347874 elements.
Creating vector time with 347874 elements.
Creating vector filter_north with 347874 elements.
Creating vector time with 347874 elements.
Creating vector filter_east with 347874 elements.
Creating vector time with 347874 elements.
Creating vector filter_depth with 347874 elements.
Creating vector time with 347874 elements.
Creating vector north_current with 347874 elements.
Creating vector time with 347874 elements.
Creating vector east_current with 347874 elements.
Creating vector time with 347874 elements.
Creating vector speed_bias with 347874 elements.
Creating vector time with 347874 elements.
Creating vector heading_bias with 347874 elements.
Creating vector time with 347874 elements.
Creating vector latitude with 347874 elements.
Creating vector time with 347874 elements.
Creating vector longitude with 347874 elements.
Creating vector time with 347874 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/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 = 13.6019
processNav(): Finding depths less than 95.2131 and times > 0
processNav(): length(Nav.depth) = 347874
processNav(): length(gindx)     = 347874
 
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/2009/2009111/2009.111.01/gps.nc')
Creating vector time with 1850 elements.
Creating vector hours with 1850 elements.
Creating vector time with 1850 elements.
Creating vector minutes with 1850 elements.
Creating vector time with 1850 elements.
Creating vector seconds with 1850 elements.
Creating vector time with 1850 elements.
Creating vector centiSeconds with 1850 elements.
Creating vector time with 1850 elements.
Creating vector latitude with 1850 elements.
Creating vector time with 1850 elements.
Creating vector longitude with 1850 elements.
Creating vector time with 1850 elements.
Creating vector quality with 1850 elements.
Creating vector time with 1850 elements.
Creating vector numberOfSatellites with 1850 elements.
Creating vector time with 1850 elements.
Creating vector hdop with 1850 elements.
Creating vector time with 1850 elements.
Creating vector antennaHeight with 1850 elements.
Creating vector time with 1850 elements.
Creating vector geoHeight with 1850 elements.
Creating vector time with 1850 elements.
Creating vector dgpsDataAge with 1850 elements.
Creating vector time with 1850 elements.
Creating vector dgpsRSID with 1850 elements.
Creating vector time with 1850 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/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/2009/2009111/2009.111.01/parosci.nc')
Creating vector time with 594046 elements.
Creating vector depth with 594046 elements.
Creating vector time with 594046 elements.
Creating vector temp with 594046 elements.
Creating vector time with 594046 elements.
Creating vector pressure with 594046 elements.
Creating vector time with 594046 elements.
Creating vector temp_period with 594046 elements.
Creating vector time with 594046 elements.
Creating vector pres_period with 594046 elements.
Creating vector time with 594046 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.95 max(Depth.data) = 29.1074
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.95 max(Depth.data) = 29.1074
[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/2009/2009111/2009.111.01/hydroscatlog.nc')
Creating vector time with 278267 elements.
Creating vector Seconds with 278267 elements.
Creating vector time with 278267 elements.
Creating vector HundrethsOfSeconds with 278267 elements.
Creating vector time with 278267 elements.
Creating vector Snorm1 with 278267 elements.
Creating vector time with 278267 elements.
Creating vector Snorm2 with 278267 elements.
Creating vector time with 278267 elements.
Creating vector Snorm3 with 278267 elements.
Creating vector time with 278267 elements.
Creating vector Gain_Status_1 with 278267 elements.
Creating vector time with 278267 elements.
Creating vector Gain_Status_2 with 278267 elements.
Creating vector time with 278267 elements.
Creating vector Gain_Status_3 with 278267 elements.
Creating vector time with 278267 elements.
Creating vector RawDepthValue with 278267 elements.
Creating vector time with 278267 elements.
Creating vector RawTempValue with 278267 elements.
Creating vector time with 278267 elements.
Creating vector Temperature with 278267 elements.
Creating vector time with 278267 elements.
Creating vector ErrorValue with 278267 elements.
Creating vector time with 278267 elements.
Creating vector bb470 with 278267 elements.
Creating vector time with 278267 elements.
Creating vector bb676 with 278267 elements.
Creating vector time with 278267 elements.
Creating vector fl676u with 278267 elements.
Creating vector time with 278267 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/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/2009/2009111/2009.111.01/ctdDriver.nc')
Creating vector time with 278178 elements.
Creating vector conductivity with 278178 elements.
Creating vector time with 278178 elements.
Creating vector temperature with 278178 elements.
Creating vector time with 278178 elements.
Creating vector cond_frequency with 278178 elements.
Creating vector time with 278178 elements.
Creating vector temp_frequency with 278178 elements.
Creating vector time with 278178 elements.
Creating vector spare with 278178 elements.
Creating vector time with 278178 elements.
Creating vector humidity with 278178 elements.
Creating vector time with 278178 elements.
Creating vector flow1 with 278178 elements.
Creating vector time with 278178 elements.
Creating vector CDOM with 278178 elements.
Creating vector time with 278178 elements.
Creating vector dissolvedO2 with 278178 elements.
Creating vector time with 278178 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/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/2009/2009111/2009.111.01/ctdDriver2.nc')
Creating vector time with 278182 elements.
Creating vector conductivity with 278182 elements.
Creating vector time with 278182 elements.
Creating vector temperature with 278182 elements.
Creating vector time with 278182 elements.
Creating vector cond_frequency with 278182 elements.
Creating vector time with 278182 elements.
Creating vector temp_frequency with 278182 elements.
Creating vector time with 278182 elements.
Creating vector flow2 with 278182 elements.
Creating vector time with 278182 elements.
Creating vector spare with 278182 elements.
Creating vector time with 278182 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/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/2009/2009111/2009.111.01/isuslog.nc')
Creating vector time with 50471 elements.
Creating vector isusNitrate with 50471 elements.
Creating vector time with 50471 elements.
Creating vector isusTemp with 50471 elements.
Creating vector time with 50471 elements.
Creating vector isusQuality with 50471 elements.
Creating vector time with 50471 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/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/2009/2009111/2009.111.01/biolume.nc')
Creating vector time with 69616 elements.
Creating vector rrr with 69616 elements.
Creating vector time with 69616 elements.
Creating vector cal_striing with 69616 elements.
Creating vector time with 69616 elements.
Creating vector pump with 69616 elements.
Creating vector time with 69616 elements.
Creating vector flow with 69616 elements.
Creating vector time with 69616 elements.
Creating vector humidity with 69616 elements.
Creating vector time with 69616 elements.
Creating vector temperature with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_0 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_1 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_2 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_3 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_4 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_5 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_6 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_7 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_8 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_9 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_10 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_11 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_12 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_13 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_14 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_15 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_16 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_17 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_18 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_19 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_20 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_21 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_22 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_23 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_24 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_25 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_26 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_27 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_28 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_29 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_30 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_31 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_32 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_33 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_34 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_35 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_36 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_37 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_38 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_39 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_40 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_41 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_42 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_43 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_44 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_45 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_46 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_47 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_48 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_49 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_50 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_51 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_52 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_53 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_54 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_55 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_56 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_57 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_58 with 69616 elements.
Creating vector time with 69616 elements.
Creating vector raw_59 with 69616 elements.
Creating vector time with 69616 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/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/2009/2009111/2009.111.01/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (5376 x 994) with 5343744 elements.
Creating vector time with 5376 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (5376 x 994) with 5343744 elements.
Creating vector time with 5376 elements.
Creating vector bin with 994 elements.
Creating matrix countList (5376 x 994) with 5343744 elements.
Creating vector time with 5376 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 5376 elements.
Creating vector time with 5376 elements.
Creating vector transCount with 5376 elements.
Creating vector time with 5376 elements.
Creating vector nonTransCount with 5376 elements.
Creating vector time with 5376 elements.
Creating vector ai_mean with 5376 elements.
Creating vector time with 5376 elements.
Creating vector ai_min with 5376 elements.
Creating vector time with 5376 elements.
Creating vector ai_max with 5376 elements.
Creating vector time with 5376 elements.
Creating vector ai_std with 5376 elements.
Creating vector time with 5376 elements.
Creating vector esd_mean with 5376 elements.
Creating vector time with 5376 elements.
Creating vector esd_min with 5376 elements.
Creating vector time with 5376 elements.
Creating vector esd_max with 5376 elements.
Creating vector time with 5376 elements.
Creating vector esd_std with 5376 elements.
Creating vector time with 5376 elements.
Creating vector countSum with 5376 elements.
Creating vector time with 5376 elements.
Creating vector snapshot with 5376 elements.
Creating vector time with 5376 elements.
Creating vector threshold with 5376 elements.
Creating vector time with 5376 elements.
Creating vector sampleCount with 5376 elements.
Creating vector time with 5376 elements.
Creating vector flowCount with 5376 elements.
Creating vector time with 5376 elements.
Creating vector flowTime with 5376 elements.
Creating vector time with 5376 elements.
Creating vector bufferStatus with 5376 elements.
Creating vector time with 5376 elements.
Creating vector laserLevel with 5376 elements.
Creating vector time with 5376 elements.
Creating vector counter with 5376 elements.
Creating vector time with 5376 elements.
Creating vector counterPeriod with 5376 elements.
Creating vector time with 5376 elements.
Creating vector laserControl with 5376 elements.
Creating vector time with 5376 elements.
Creating vector countUnknownFrameCharacter with 5376 elements.
Creating vector time with 5376 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 5376 elements.
Creating vector time with 5376 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 5376 elements.
Creating vector time with 5376 elements.
Creating vector flowSpeed with 5376 elements.
Creating vector time with 5376 elements.
Creating vector countShortLFrameError with 5376 elements.
Creating vector time with 5376 elements.
Creating vector countGarbledLFrame with 5376 elements.
Creating vector time with 5376 elements.
Creating vector correctedSampleCountList with 5376 elements.
Creating vector time with 5376 elements.
Creating vector time with 5376 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2009/2009111/2009.111.01/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009.111.01.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_2009.111.01.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 45 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_2009_111_01_111_01_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_2009_111_01_111_01.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01.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 = 762 Gridding with nix = 2286, iZ = 55
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
     count
     transCount
     nonTransCount
     LCcount
 
Masking and filtering with median filter of size 5...
  cvarname = gT
  cvarname = gS
  cvarname = gO
  cvarname = gN
  cvarname = gF
  cvarname = gB420
  cvarname = gB700
  cvarname = gBL
  cvarname = gBLflow
  cvarname = gLOPCcount
  cvarname = gLOPCtransCount
  cvarname = gLOPCnonTransCount
  cvarname = gLOPCLCcount
Encountered 0 NaN values in array of lon that is 347757 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 347757 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 119016 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 04/21/2009 12:30  to 04/22/2009 10:29 

swr =

  952.6836
  927.1696
  823.6071
  690.7840
  536.6404
  351.9431
  187.9040
   33.8677
    2.8499
    2.7000
    2.8752
    2.6000
    3.0504
    2.8752
    2.9624
    2.7120
    2.9220
    3.4248
   12.9279
   64.8729
  148.2866
  234.0091
  416.4461

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2009111_GulperTimes.txt && touch ../results/2009111_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/2009/2009111/2009.111.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2009/2009111/2009.111.01/syslog -startEsecs 1240350284.9989 -surveyName Dorado389_2009_111_01_111_01 >> ../results/2009111_GulperTimes.txt
Executing: removeGulpDups.py ../results/2009111_GulperTimes.txt
Bottle: 0 Time: 1240402919 Depth: 6.0818 Dist: 59.7846
Bottle: 1 Time: 1240404216 Depth: 5.628 Dist: 61.2257
Bottle: 2 Time: 1240405218 Depth: 5.9081 Dist: 62.3354
Bottle: 3 Time: 1240406374 Depth: 6.0852 Dist: 63.6516
Bottle: 4 Time: 1240407485.2004 Depth: 5.8984 Dist: 64.8422
Bottle: 5 Time: 1240411091 Depth: 5.4551 Dist: 69.0026
Bottle: 6 Time: 1240414847 Depth: 5.8509 Dist: 73.3042
Bottle: 7 Time: 1240416546 Depth: 5.9763 Dist: 75.1911
Bottle: 8 Time: 1240418216 Depth: 6.0418 Dist: 77.1503
Bottle: 9 Time: 1240419768 Depth: 4.2434 Dist: 79.0541
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_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
  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 gB420
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB700
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gF
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_2column.png
Elapsed time to save image: 13 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 gB420
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gB700
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gF
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_biolume.png
Elapsed time to save image: 52 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 gB420
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB700
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gF
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_lopc.png
Elapsed time to save image: 15 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_2009_111_01_111_01_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_2column.png...
Copied to /mbari/AUVCTD/surveys/2009/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_biolume.png...
Copied to /mbari/AUVCTD/surveys/2009/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_lopc.png...
Copied to /mbari/AUVCTD/surveys/2009/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2009/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2009/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2009/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_2009_111_01_111_01_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_111_01_111_01_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2009/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_2009_111_01_111_01_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_111_01_111_01_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2009/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_2009_111_01_111_01_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_111_01_111_01_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2009/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_2009_111_01_111_01_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_111_01_111_01_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2009/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_2009_111_01_111_01_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_111_01_111_01_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2009/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_2009_111_01_111_01_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_111_01_111_01_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2009/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_2009_111_01_111_01_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_111_01_111_01_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2009/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_2009_111_01_111_01_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_111_01_111_01_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2009/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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_111_01_111_01_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_111_01_111_01_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2009/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2009_111_01_111_01.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01.kml...
Copied to /mbari/AUVCTD/surveys/2009/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2009_111_01_111_01_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_2009_111_01_111_01.mat ...
Iterpolating to isus time values...
Interpolating ctd2 temperature...
Interpolating ctd2 salinity...
1 NaNs found in bbpBlue.  Interpolating anyway.
5 NaNs found in bbpRed.  Interpolating anyway.
2 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 18 NaN values in array of lon that is 50471 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 50453 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 50453 are not equal to number of Lat lon points = 50471
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_2009_111_01_111_01.txt
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01.txt...
Copied to /mbari/AUVCTD/surveys/2009/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2009/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd2 temperature...
Interpolating ctd2 salinity...
1 NaNs found in bbpBlue.  Interpolating anyway.
5 NaNs found in bbpRed.  Interpolating anyway.
2 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_2009_111_01_111_01_decim.nc...
Copied to /mbari/AUVCTD/surveys/2009/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_2009_111_01_111_01.nc...
Copied to /mbari/AUVCTD/surveys/2009/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2009/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009_111_01_111_01.mat...
Copied to /mbari/AUVCTD/surveys/2009/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2009_111_01_111_01 processed" mccann@mbari.org < mail_Dorado389_2009_111_01_111_01.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2009.111.01.mat
Processing time: 641 seconds