Execution of AUVprocess_main version 1.88 at 2019-12-18T23:41:20Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2019, ['350.01'], '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: 2019.350.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/
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/2019/2019350/2019.350.01/navigation.nc')
Creating vector time with 93292 elements.
Creating vector mPos_x with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mPos_y with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mDepth with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mGpsNorth with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mGpsEast with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mGpsValid with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mPhi with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mTheta with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mPsi with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mOmega_x with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mOmega_y with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mOmega_z with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mPsaRange with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mAltitude with 93292 elements.
Creating vector time with 93292 elements.
Creating vector multibeamAltitude with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mDvlAltitude with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mEchoAltitude with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mEchoHorizRange with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mEchoAltitudeLast with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mEchoHorizRangeLast with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mEchoNumOfPings with 93292 elements.
Creating vector time with 93292 elements.
Creating vector nadirCnts with 93292 elements.
Creating vector time with 93292 elements.
Creating vector obstacleCnts with 93292 elements.
Creating vector time with 93292 elements.
Creating vector nGoodNadirBeams with 93292 elements.
Creating vector time with 93292 elements.
Creating vector medianNadirBeamNo with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mWaterSpeed with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mDvlValid with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mDvlNewData with 93292 elements.
Creating vector time with 93292 elements.
Creating vector mDeltaT with 93292 elements.
Creating vector time with 93292 elements.
Creating vector nfix with 93292 elements.
Creating vector time with 93292 elements.
Creating vector efix with 93292 elements.
Creating vector time with 93292 elements.
Creating vector filter_north with 93292 elements.
Creating vector time with 93292 elements.
Creating vector filter_east with 93292 elements.
Creating vector time with 93292 elements.
Creating vector filter_depth with 93292 elements.
Creating vector time with 93292 elements.
Creating vector north_current with 93292 elements.
Creating vector time with 93292 elements.
Creating vector east_current with 93292 elements.
Creating vector time with 93292 elements.
Creating vector speed_bias with 93292 elements.
Creating vector time with 93292 elements.
Creating vector heading_bias with 93292 elements.
Creating vector time with 93292 elements.
Creating vector latitude with 93292 elements.
Creating vector time with 93292 elements.
Creating vector longitude with 93292 elements.
Creating vector time with 93292 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/navigation.nc');
processNav(): median of positive valued depths = 31.0245
processNav(): Finding depths less than 217.1713 and times > 0
processNav(): length(Nav.depth) = 93292
processNav(): length(gindx)     = 93292
 
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/2019/2019350/2019.350.01/gps.nc')
Creating vector time with 7547 elements.
Creating vector hours with 7547 elements.
Creating vector time with 7547 elements.
Creating vector minutes with 7547 elements.
Creating vector time with 7547 elements.
Creating vector seconds with 7547 elements.
Creating vector time with 7547 elements.
Creating vector centiSeconds with 7547 elements.
Creating vector time with 7547 elements.
Creating vector latitude with 7547 elements.
Creating vector time with 7547 elements.
Creating vector longitude with 7547 elements.
Creating vector time with 7547 elements.
Creating vector quality with 7547 elements.
Creating vector time with 7547 elements.
Creating vector numberOfSatellites with 7547 elements.
Creating vector time with 7547 elements.
Creating vector hdop with 7547 elements.
Creating vector time with 7547 elements.
Creating vector antennaHeight with 7547 elements.
Creating vector time with 7547 elements.
Creating vector geoHeight with 7547 elements.
Creating vector time with 7547 elements.
Creating vector dgpsDataAge with 7547 elements.
Creating vector time with 7547 elements.
Creating vector dgpsRSID with 7547 elements.
Creating vector time with 7547 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/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/2019/2019350/2019.350.01/parosci.nc')
Creating vector time with 186050 elements.
Creating vector depth with 186050 elements.
Creating vector time with 186050 elements.
Creating vector temp with 186050 elements.
Creating vector time with 186050 elements.
Creating vector pressure with 186050 elements.
Creating vector time with 186050 elements.
Creating vector temp_period with 186050 elements.
Creating vector time with 186050 elements.
Creating vector pres_period with 186050 elements.
Creating vector time with 186050 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.24942 max(Depth.data) = 202.4231
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.24942 max(Depth.data) = 202.4231
 
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/2019/2019350/2019.350.01/hydroscatlog.nc')
Creating vector time with 74732 elements.
Creating vector Seconds with 74732 elements.
Creating vector time with 74732 elements.
Creating vector HundrethsOfSeconds with 74732 elements.
Creating vector time with 74732 elements.
Creating vector Snorm1 with 74732 elements.
Creating vector time with 74732 elements.
Creating vector Snorm2 with 74732 elements.
Creating vector time with 74732 elements.
Creating vector Snorm3 with 74732 elements.
Creating vector time with 74732 elements.
Creating vector Gain_Status_1 with 74732 elements.
Creating vector time with 74732 elements.
Creating vector Gain_Status_2 with 74732 elements.
Creating vector time with 74732 elements.
Creating vector Gain_Status_3 with 74732 elements.
Creating vector time with 74732 elements.
Creating vector RawDepthValue with 74732 elements.
Creating vector time with 74732 elements.
Creating vector RawTempValue with 74732 elements.
Creating vector time with 74732 elements.
Creating vector Temperature with 74732 elements.
Creating vector time with 74732 elements.
Creating vector ErrorValue with 74732 elements.
Creating vector time with 74732 elements.
Creating vector bb470 with 74732 elements.
Creating vector time with 74732 elements.
Creating vector bb676 with 74732 elements.
Creating vector time with 74732 elements.
Creating vector fl676u with 74732 elements.
Creating vector time with 74732 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/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/2019/2019350/2019.350.01/ctdDriver.nc')
Creating vector time with 74679 elements.
Creating vector conductivity with 74679 elements.
Creating vector time with 74679 elements.
Creating vector temperature with 74679 elements.
Creating vector time with 74679 elements.
Creating vector cond_frequency with 74679 elements.
Creating vector time with 74679 elements.
Creating vector temp_frequency with 74679 elements.
Creating vector time with 74679 elements.
Creating vector spare with 74679 elements.
Creating vector time with 74679 elements.
Creating vector humidity with 74679 elements.
Creating vector time with 74679 elements.
Creating vector flow1 with 74679 elements.
Creating vector time with 74679 elements.
Creating vector CDOM with 74679 elements.
Creating vector time with 74679 elements.
Creating vector dissolvedO2 with 74679 elements.
Creating vector time with 74679 elements.
Creating vector salinity with 74679 elements.
Creating vector time with 74679 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/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/2019/2019350/2019.350.01/ctdDriver2.nc')
Creating vector time with 74675 elements.
Creating vector conductivity with 74675 elements.
Creating vector time with 74675 elements.
Creating vector temperature with 74675 elements.
Creating vector time with 74675 elements.
Creating vector cond_frequency with 74675 elements.
Creating vector time with 74675 elements.
Creating vector temp_frequency with 74675 elements.
Creating vector time with 74675 elements.
Creating vector flow2 with 74675 elements.
Creating vector time with 74675 elements.
Creating vector spare with 74675 elements.
Creating vector time with 74675 elements.
Creating vector salinity with 74675 elements.
Creating vector time with 74675 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/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/2019/2019350/2019.350.01/isuslog.nc')
Creating vector time with 14509 elements.
Creating vector isusNitrate with 14509 elements.
Creating vector time with 14509 elements.
Creating vector isusTemp with 14509 elements.
Creating vector time with 14509 elements.
Creating vector isusQuality with 14509 elements.
Creating vector time with 14509 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/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 71)
  In processBiolume (line 21)
  In processAUVmission (line 220)
  In AUVprocess_main (line 227)] 
[Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 71)
  In processBiolume (line 22)
  In processAUVmission (line 220)
  In AUVprocess_main (line 227)] 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/biolume.nc')
Creating vector time with 18382 elements.
Creating vector rrr with 18382 elements.
Creating vector time with 18382 elements.
Creating vector cal_striing with 18382 elements.
Creating vector time with 18382 elements.
Creating vector avg_biolume with 18382 elements.
Creating vector time with 18382 elements.
Creating vector pump with 18382 elements.
Creating vector time with 18382 elements.
Creating vector system_voltage with 18382 elements.
Creating vector time with 18382 elements.
Creating vector flow with 18382 elements.
Creating vector time with 18382 elements.
Creating vector HV with 18382 elements.
Creating vector time with 18382 elements.
Creating vector reserved with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_0 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_1 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_2 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_3 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_4 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_5 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_6 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_7 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_8 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_9 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_10 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_11 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_12 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_13 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_14 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_15 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_16 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_17 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_18 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_19 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_20 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_21 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_22 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_23 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_24 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_25 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_26 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_27 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_28 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_29 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_30 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_31 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_32 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_33 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_34 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_35 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_36 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_37 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_38 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_39 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_40 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_41 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_42 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_43 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_44 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_45 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_46 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_47 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_48 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_49 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_50 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_51 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_52 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_53 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_54 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_55 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_56 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_57 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_58 with 18382 elements.
Creating vector time with 18382 elements.
Creating vector raw_59 with 18382 elements.
Creating vector time with 18382 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/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/2019/2019350/2019.350.01/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (1780 x 994) with 1769320 elements.
Creating vector time with 1780 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (1780 x 994) with 1769320 elements.
Creating vector time with 1780 elements.
Creating vector bin with 994 elements.
Creating matrix countList (1780 x 994) with 1769320 elements.
Creating vector time with 1780 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 1780 elements.
Creating vector time with 1780 elements.
Creating vector transCount with 1780 elements.
Creating vector time with 1780 elements.
Creating vector nonTransCount with 1780 elements.
Creating vector time with 1780 elements.
Creating vector ai_mean with 1780 elements.
Creating vector time with 1780 elements.
Creating vector ai_min with 1780 elements.
Creating vector time with 1780 elements.
Creating vector ai_max with 1780 elements.
Creating vector time with 1780 elements.
Creating vector ai_std with 1780 elements.
Creating vector time with 1780 elements.
Creating vector esd_mean with 1780 elements.
Creating vector time with 1780 elements.
Creating vector esd_min with 1780 elements.
Creating vector time with 1780 elements.
Creating vector esd_max with 1780 elements.
Creating vector time with 1780 elements.
Creating vector esd_std with 1780 elements.
Creating vector time with 1780 elements.
Creating vector countSum with 1780 elements.
Creating vector time with 1780 elements.
Creating vector snapshot with 1780 elements.
Creating vector time with 1780 elements.
Creating vector threshold with 1780 elements.
Creating vector time with 1780 elements.
Creating vector sampleCount with 1780 elements.
Creating vector time with 1780 elements.
Creating vector flowCount with 1780 elements.
Creating vector time with 1780 elements.
Creating vector flowTime with 1780 elements.
Creating vector time with 1780 elements.
Creating vector bufferStatus with 1780 elements.
Creating vector time with 1780 elements.
Creating vector laserLevel with 1780 elements.
Creating vector time with 1780 elements.
Creating vector counter with 1780 elements.
Creating vector time with 1780 elements.
Creating vector counterPeriod with 1780 elements.
Creating vector time with 1780 elements.
Creating vector laserControl with 1780 elements.
Creating vector time with 1780 elements.
Creating vector countUnknownFrameCharacter with 1780 elements.
Creating vector time with 1780 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 1780 elements.
Creating vector time with 1780 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 1780 elements.
Creating vector time with 1780 elements.
Creating vector flowSpeed with 1780 elements.
Creating vector time with 1780 elements.
Creating vector countShortLFrameError with 1780 elements.
Creating vector time with 1780 elements.
Creating vector countGarbledLFrame with 1780 elements.
Creating vector time with 1780 elements.
Creating vector cFrameEsecs with 1780 elements.
Creating vector time with 1780 elements.
Creating vector correctedSampleCountList with 1780 elements.
Creating vector time with 1780 elements.
Creating vector time with 1780 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019350/2019.350.01/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019.350.01.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_2019.350.01.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_2019_350_01_350_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 624)
  In imwrite (line 440)
  In matlab.graphics.internal.mlprintjob/writeRaster
  In printingGenerateOutput
  In alternatePrintPath
  In print (line 82)
  In create_data_products (line 98)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 257)] 
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_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 = 54 Gridding with nix = 162, iZ = 402
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 42034 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 42034 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 120672 elements.
*** Could not find start or end index in Met data read from http://elvis.shore.mbari.org/thredds/dodsC/agg/OS_MBARI-M1_R_M
Looking for start days = 25551.8064 since 1/1/1950
Looking for end   days = 25552.0223
sIndx = 
eIndx = 
Met data goes from 20017.6042 to 25054.7292
No SWR data loaded from URL.
Executing: /bin/rm -f ../results/2019350_GulperTimes.txt && touch ../results/2019350_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/2019/2019350/2019.350.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2019/2019350/2019.350.01/syslog -startEsecs 1576524071.5078 -surveyName Dorado389_2019_350_01_350_01 >> ../results/2019350_GulperTimes.txt
Executing: removeGulpDups.py ../results/2019350_GulperTimes.txt
Bottle: 0 Time: 1576526025.7039 Depth: 200.1978 Dist: 1.6711
Bottle: 1 Time: 1576526145.5057 Depth: 149.7668 Dist: 1.7934
Bottle: 2 Time: 1576526252.7084 Depth: 99.7164 Dist: 1.8974
Bottle: 3 Time: 1576526300.1051 Depth: 79.7915 Dist: 1.9357
Bottle: 4 Time: 1576526352.5015 Depth: 59.7645 Dist: 1.9889
Bottle: 5 Time: 1576526402.1081 Depth: 39.7602 Dist: 2.036
Bottle: 6 Time: 1576526431.5061 Depth: 29.7471 Dist: 2.0555
Bottle: 7 Time: 1576526461.844 Depth: 19.6046 Dist: 2.0908
Bottle: 8 Time: 1576526492.302 Depth: 9.7487 Dist: 2.1275
Bottle: 9 Time: 1576527845.905 Depth: -0.01354 Dist: 2.6327
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_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 '

[Warning: P-file /mbari/matlab/toolbox/matlab/imagesci/imread.p is older than
MATLAB file /mbari/matlab/toolbox/matlab/imagesci/imread.m.
/mbari/matlab/toolbox/matlab/imagesci/imread.p may be obsolete and may need to
be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In plot_sections (line 782)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 257)] 
[Warning: P-file /mbari/matlab/toolbox/matlab/imagesci/private/imjpginfo.p is
older than MATLAB file
/mbari/matlab/toolbox/matlab/imagesci/private/imjpginfo.m.
/mbari/matlab/toolbox/matlab/imagesci/private/imjpginfo.p may be obsolete and
may need to be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In readjpg (line 7)
  In imread
  In imread
  In plot_sections (line 782)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 257)] 
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
Did not add swr plot to the image.
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_2column.png
Elapsed time to save image: 8 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
SWR image not added to the plot.
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_biolume.png
Elapsed time to save image: 22 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
Did not add swr plot to the image.
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_lopc.png
Elapsed time to save image: 7 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_2019_350_01_350_01_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_2column.png...
Copied to /mbari/AUVCTD/surveys/2019/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_biolume.png...
Copied to /mbari/AUVCTD/surveys/2019/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_lopc.png...
Copied to /mbari/AUVCTD/surveys/2019/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2019/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2019/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2019/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_2019_350_01_350_01_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_350_01_350_01_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2019/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_2019_350_01_350_01_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_350_01_350_01_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2019/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_2019_350_01_350_01_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_350_01_350_01_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2019/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_2019_350_01_350_01_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_350_01_350_01_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2019/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_2019_350_01_350_01_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_350_01_350_01_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2019/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_2019_350_01_350_01_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_350_01_350_01_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2019/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_2019_350_01_350_01_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_350_01_350_01_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2019/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_2019_350_01_350_01_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_350_01_350_01_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2019/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_2019_350_01_350_01_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_350_01_350_01_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2019/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2019_350_01_350_01.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01.kml...
Copied to /mbari/AUVCTD/surveys/2019/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_350_01_350_01_LOPC_Total_Count.kml'
not found.] 
[> In create_data_products (line 419)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 257)] 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
1 NaNs found in bbpRed.  Interpolating anyway.
Encountered 7986 NaN values in array of lon that is 14500 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 6514 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 6514 are not equal to number of Lat lon points = 14500
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_2019_350_01_350_01.txt
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01.txt...
Copied to /mbari/AUVCTD/surveys/2019/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2019/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
1 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_decim.nc...
Copied to /mbari/AUVCTD/surveys/2019/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_2019_350_01_350_01.nc...
Copied to /mbari/AUVCTD/surveys/2019/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2019/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_350_01_350_01.mat...
Copied to /mbari/AUVCTD/surveys/2019/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2019_350_01_350_01 processed" mccann@mbari.org < mail_Dorado389_2019_350_01_350_01.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019.350.01.mat
Processing time: 52 seconds