Execution of AUVprocess_main version 1.88 at 2021-07-30T20:46:04Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2017, ['304.00'], '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: 2017.304.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/
Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd.cvs/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/2017/2017304/2017.304.00/navigation.nc')
Creating vector time with 411971 elements.
Creating vector mPos_x with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mPos_y with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mDepth with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mGpsNorth with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mGpsEast with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mGpsValid with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mPhi with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mTheta with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mPsi with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mOmega_x with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mOmega_y with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mOmega_z with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mPsaRange with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mAltitude with 411971 elements.
Creating vector time with 411971 elements.
Creating vector multibeamAltitude with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mDvlAltitude with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mEchoAltitude with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mEchoHorizRange with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mEchoAltitudeLast with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mEchoHorizRangeLast with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mEchoNumOfPings with 411971 elements.
Creating vector time with 411971 elements.
Creating vector nadirCnts with 411971 elements.
Creating vector time with 411971 elements.
Creating vector obstacleCnts with 411971 elements.
Creating vector time with 411971 elements.
Creating vector nGoodNadirBeams with 411971 elements.
Creating vector time with 411971 elements.
Creating vector medianNadirBeamNo with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mWaterSpeed with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mDvlValid with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mDvlNewData with 411971 elements.
Creating vector time with 411971 elements.
Creating vector mDeltaT with 411971 elements.
Creating vector time with 411971 elements.
Creating vector nfix with 411971 elements.
Creating vector time with 411971 elements.
Creating vector efix with 411971 elements.
Creating vector time with 411971 elements.
Creating vector filter_north with 411971 elements.
Creating vector time with 411971 elements.
Creating vector filter_east with 411971 elements.
Creating vector time with 411971 elements.
Creating vector filter_depth with 411971 elements.
Creating vector time with 411971 elements.
Creating vector north_current with 411971 elements.
Creating vector time with 411971 elements.
Creating vector east_current with 411971 elements.
Creating vector time with 411971 elements.
Creating vector speed_bias with 411971 elements.
Creating vector time with 411971 elements.
Creating vector heading_bias with 411971 elements.
Creating vector time with 411971 elements.
Creating vector latitude with 411971 elements.
Creating vector time with 411971 elements.
Creating vector longitude with 411971 elements.
Creating vector time with 411971 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/navigation.nc');
processNav(): median of positive valued depths = 31.4026
processNav(): Finding depths less than 314.0264 and times > 0
processNav(): length(Nav.depth) = 411971
processNav(): length(gindx)     = 411970
 
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/2017/2017304/2017.304.00/gps.nc')
Creating vector time with 8762 elements.
Creating vector hours with 8762 elements.
Creating vector time with 8762 elements.
Creating vector minutes with 8762 elements.
Creating vector time with 8762 elements.
Creating vector seconds with 8762 elements.
Creating vector time with 8762 elements.
Creating vector centiSeconds with 8762 elements.
Creating vector time with 8762 elements.
Creating vector latitude with 8762 elements.
Creating vector time with 8762 elements.
Creating vector longitude with 8762 elements.
Creating vector time with 8762 elements.
Creating vector quality with 8762 elements.
Creating vector time with 8762 elements.
Creating vector numberOfSatellites with 8762 elements.
Creating vector time with 8762 elements.
Creating vector hdop with 8762 elements.
Creating vector time with 8762 elements.
Creating vector antennaHeight with 8762 elements.
Creating vector time with 8762 elements.
Creating vector geoHeight with 8762 elements.
Creating vector time with 8762 elements.
Creating vector dgpsDataAge with 8762 elements.
Creating vector time with 8762 elements.
Creating vector dgpsRSID with 8762 elements.
Creating vector time with 8762 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/gps.nc');
processGPS(): *** skipping bad position (lat,lon) = 60.7827, -121.9619
processGPS(): *** skipping bad position (lat,lon) = 60.817, -121.9644
processGPS(): *** skipping bad position (lat,lon) = 60.8513, -121.9669
processGPS(): *** skipping bad position (lat,lon) = 62.6835, -122.1234
processGPS(): *** skipping bad position (lat,lon) = 62.7171, -122.1267
processGPS(): *** skipping bad position (lat,lon) = 62.7506, -122.13
processGPS(): *** skipping bad position (lat,lon) = 63.2189, -122.1782
processGPS(): *** skipping bad position (lat,lon) = 63.2522, -122.1817
processGPS(): *** skipping bad position (lat,lon) = 63.2856, -122.1853
processGPS(): *** skipping bad position (lat,lon) = 63.3189, -122.1889
processGPS(): *** skipping bad position (lat,lon) = 63.3522, -122.1925
 
Processing depth data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/parosci.nc')
Creating vector time with 808787 elements.
Creating vector depth with 808787 elements.
Creating vector time with 808787 elements.
Creating vector temp with 808787 elements.
Creating vector time with 808787 elements.
Creating vector pressure with 808787 elements.
Creating vector time with 808787 elements.
Creating vector temp_period with 808787 elements.
Creating vector time with 808787 elements.
Creating vector pres_period with 808787 elements.
Creating vector time with 808787 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.23115 max(Depth.data) = 204.27
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.23115 max(Depth.data) = 204.27
 
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/2017/2017304/2017.304.00/hydroscatlog.nc')
Creating vector time with 132893 elements.
Creating vector Seconds with 132893 elements.
Creating vector time with 132893 elements.
Creating vector HundrethsOfSeconds with 132893 elements.
Creating vector time with 132893 elements.
Creating vector Snorm1 with 132893 elements.
Creating vector time with 132893 elements.
Creating vector Snorm2 with 132893 elements.
Creating vector time with 132893 elements.
Creating vector Snorm3 with 132893 elements.
Creating vector time with 132893 elements.
Creating vector Gain_Status_1 with 132893 elements.
Creating vector time with 132893 elements.
Creating vector Gain_Status_2 with 132893 elements.
Creating vector time with 132893 elements.
Creating vector Gain_Status_3 with 132893 elements.
Creating vector time with 132893 elements.
Creating vector RawDepthValue with 132893 elements.
Creating vector time with 132893 elements.
Creating vector RawTempValue with 132893 elements.
Creating vector time with 132893 elements.
Creating vector Temperature with 132893 elements.
Creating vector time with 132893 elements.
Creating vector ErrorValue with 132893 elements.
Creating vector time with 132893 elements.
Creating vector bb470 with 132893 elements.
Creating vector time with 132893 elements.
Creating vector bb676 with 132893 elements.
Creating vector time with 132893 elements.
Creating vector fl676u with 132893 elements.
Creating vector time with 132893 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/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/2017/2017304/2017.304.00/ctdDriver.nc')
Creating vector time with 327376 elements.
Creating vector conductivity with 327376 elements.
Creating vector time with 327376 elements.
Creating vector temperature with 327376 elements.
Creating vector time with 327376 elements.
Creating vector cond_frequency with 327376 elements.
Creating vector time with 327376 elements.
Creating vector temp_frequency with 327376 elements.
Creating vector time with 327376 elements.
Creating vector spare with 327376 elements.
Creating vector time with 327376 elements.
Creating vector humidity with 327376 elements.
Creating vector time with 327376 elements.
Creating vector flow1 with 327376 elements.
Creating vector time with 327376 elements.
Creating vector CDOM with 327376 elements.
Creating vector time with 327376 elements.
Creating vector dissolvedO2 with 327376 elements.
Creating vector time with 327376 elements.
Creating vector salinity with 327376 elements.
Creating vector time with 327376 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/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/2017/2017304/2017.304.00/ctdDriver2.nc')
Creating vector time with 327409 elements.
Creating vector conductivity with 327409 elements.
Creating vector time with 327409 elements.
Creating vector temperature with 327409 elements.
Creating vector time with 327409 elements.
Creating vector cond_frequency with 327409 elements.
Creating vector time with 327409 elements.
Creating vector temp_frequency with 327409 elements.
Creating vector time with 327409 elements.
Creating vector flow2 with 327409 elements.
Creating vector time with 327409 elements.
Creating vector spare with 327409 elements.
Creating vector time with 327409 elements.
Creating vector salinity with 327409 elements.
Creating vector time with 327409 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/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/2017/2017304/2017.304.00/isuslog.nc')
Creating vector time with 64196 elements.
Creating vector isusNitrate with 64196 elements.
Creating vector time with 64196 elements.
Creating vector isusTemp with 64196 elements.
Creating vector time with 64196 elements.
Creating vector isusQuality with 64196 elements.
Creating vector time with 64196 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/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 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/2017/2017304/2017.304.00/biolume.nc')
Creating vector time with 80985 elements.
Creating vector rrr with 80985 elements.
Creating vector time with 80985 elements.
Creating vector cal_striing with 80985 elements.
Creating vector time with 80985 elements.
Creating vector avg_biolume with 80985 elements.
Creating vector time with 80985 elements.
Creating vector pump with 80985 elements.
Creating vector time with 80985 elements.
Creating vector system_voltage with 80985 elements.
Creating vector time with 80985 elements.
Creating vector flow with 80985 elements.
Creating vector time with 80985 elements.
Creating vector HV with 80985 elements.
Creating vector time with 80985 elements.
Creating vector reserved with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_0 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_1 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_2 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_3 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_4 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_5 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_6 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_7 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_8 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_9 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_10 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_11 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_12 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_13 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_14 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_15 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_16 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_17 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_18 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_19 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_20 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_21 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_22 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_23 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_24 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_25 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_26 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_27 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_28 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_29 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_30 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_31 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_32 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_33 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_34 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_35 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_36 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_37 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_38 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_39 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_40 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_41 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_42 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_43 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_44 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_45 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_46 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_47 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_48 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_49 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_50 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_51 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_52 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_53 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_54 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_55 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_56 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_57 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_58 with 80985 elements.
Creating vector time with 80985 elements.
Creating vector raw_59 with 80985 elements.
Creating vector time with 80985 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/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/2017/2017304/2017.304.00/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (7849 x 994) with 7801906 elements.
Creating vector time with 7849 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (7849 x 994) with 7801906 elements.
Creating vector time with 7849 elements.
Creating vector bin with 994 elements.
Creating matrix countList (7849 x 994) with 7801906 elements.
Creating vector time with 7849 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 7849 elements.
Creating vector time with 7849 elements.
Creating vector transCount with 7849 elements.
Creating vector time with 7849 elements.
Creating vector nonTransCount with 7849 elements.
Creating vector time with 7849 elements.
Creating vector ai_mean with 7849 elements.
Creating vector time with 7849 elements.
Creating vector ai_min with 7849 elements.
Creating vector time with 7849 elements.
Creating vector ai_max with 7849 elements.
Creating vector time with 7849 elements.
Creating vector ai_std with 7849 elements.
Creating vector time with 7849 elements.
Creating vector esd_mean with 7849 elements.
Creating vector time with 7849 elements.
Creating vector esd_min with 7849 elements.
Creating vector time with 7849 elements.
Creating vector esd_max with 7849 elements.
Creating vector time with 7849 elements.
Creating vector esd_std with 7849 elements.
Creating vector time with 7849 elements.
Creating vector countSum with 7849 elements.
Creating vector time with 7849 elements.
Creating vector snapshot with 7849 elements.
Creating vector time with 7849 elements.
Creating vector threshold with 7849 elements.
Creating vector time with 7849 elements.
Creating vector sampleCount with 7849 elements.
Creating vector time with 7849 elements.
Creating vector flowCount with 7849 elements.
Creating vector time with 7849 elements.
Creating vector flowTime with 7849 elements.
Creating vector time with 7849 elements.
Creating vector bufferStatus with 7849 elements.
Creating vector time with 7849 elements.
Creating vector laserLevel with 7849 elements.
Creating vector time with 7849 elements.
Creating vector counter with 7849 elements.
Creating vector time with 7849 elements.
Creating vector counterPeriod with 7849 elements.
Creating vector time with 7849 elements.
Creating vector laserControl with 7849 elements.
Creating vector time with 7849 elements.
Creating vector countUnknownFrameCharacter with 7849 elements.
Creating vector time with 7849 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7849 elements.
Creating vector time with 7849 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7849 elements.
Creating vector time with 7849 elements.
Creating vector flowSpeed with 7849 elements.
Creating vector time with 7849 elements.
Creating vector countShortLFrameError with 7849 elements.
Creating vector time with 7849 elements.
Creating vector countGarbledLFrame with 7849 elements.
Creating vector time with 7849 elements.
Creating vector cFrameEsecs with 7849 elements.
Creating vector time with 7849 elements.
Creating vector correctedSampleCountList with 7849 elements.
Creating vector time with 7849 elements.
Creating vector time with 7849 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017304/2017.304.00/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017.304.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Calling build_auv_survey.m to construct survey file...
Reading: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017.304.00.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 30 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.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00.mat
Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_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 = 414 Gridding with nix = 1242, iZ = 406
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 404765 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 404765 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 145548 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 10/31/2017 08:30  to 11/01/2017 09:30 

swr =

   34.8988
   98.9862
  157.6930
  274.2852
  362.3434
  405.3177
  425.6934
  369.9354
  215.5197
   62.7258
    2.5886
    0.9128
    1.0205
    0.9836
    0.7000
    0.9092
    0.6241
    0.6574
    0.7093
    0.8554
    1.2000
    1.2185
    1.4815
    9.6097
   88.9709
  288.0842

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2017304_GulperTimes.txt && touch ../results/2017304_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/2017/2017304/2017.304.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2017/2017304/2017.304.00/syslog -startEsecs 1509470110.8791 -surveyName Dorado389_2017_304_00_304_00 >> ../results/2017304_GulperTimes.txt
Executing: removeGulpDups.py ../results/2017304_GulperTimes.txt
Bottle: 0 Time: 1509471710.8795 Depth: 200.0869 Dist: 1.8654
Bottle: 1 Time: 1509471858.8793 Depth: 149.9492 Dist: 2.0645
Bottle: 2 Time: 1509471995.48 Depth: 99.9522 Dist: 2.2459
Bottle: 3 Time: 1509472059.4756 Depth: 79.929 Dist: 2.3254
Bottle: 4 Time: 1509472123.0712 Depth: 59.9356 Dist: 2.4118
Bottle: 5 Time: 1509472184.677 Depth: 39.9557 Dist: 2.499
Bottle: 6 Time: 1509472222.8744 Depth: 29.9617 Dist: 2.5538
Bottle: 7 Time: 1509472261.6718 Depth: 19.9097 Dist: 2.6046
Bottle: 8 Time: 1509472303.0789 Depth: 9.9454 Dist: 2.6622
Bottle: 9 Time: 1509472364.8847 Depth: -0.030962 Dist: 2.7194
Bottle: 10 Time: 1509508413.4752 Depth: 200.0521 Dist: 38.7076
Bottle: 11 Time: 1509508547.076 Depth: 149.9519 Dist: 38.877
Bottle: 12 Time: 1509508678.477 Depth: 99.9502 Dist: 39.0319
Bottle: 13 Time: 1509508740.8728 Depth: 79.934 Dist: 39.1024
Bottle: 14 Time: 1509508802.6785 Depth: 59.9496 Dist: 39.1877
Bottle: 15 Time: 1509508864.4743 Depth: 39.9497 Dist: 39.2636
Bottle: 16 Time: 1509508901.4718 Depth: 29.9558 Dist: 39.3026
Bottle: 17 Time: 1509508940.0791 Depth: 19.9919 Dist: 39.3436
Bottle: 18 Time: 1509508979.2764 Depth: 9.911 Dist: 39.3919
Bottle: 19 Time: 1509509211.8905 Depth: -0.085276 Dist: 39.4961
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_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
  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.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_2column.png
Elapsed time to save image: 10 seconds
Biolume contouring gridded variable gD
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gT
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gS
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gN
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gO
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable 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.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_biolume.png
Elapsed time to save image: 38 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.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_lopc.png
Elapsed time to save image: 11 seconds
 
 
*************************************************************************
Calling plot_survey_stats to produce histogram and profile statistics plots...
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_2column.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_biolume.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_lopc.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd2 temperature...
Interpolating ctd2 salinity...
5 NaNs found in bbpBlue.  Interpolating anyway.
5 NaNs found in bbpRed.  Interpolating anyway.
3 NaNs found in flRed_uncorr.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_decim.nc...
Copied to /mbari/AUVCTD/surveys/2017/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
Creating Dorado389_2017_304_00_304_00.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00.kml...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_304_00_304_00_LOPC_Total_Count.kml'
not found.] 
[> In create_data_products (line 445)
  In build_auv_survey (line 530)
  In AUVprocess_main (line 257)] 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00.mat ...
Iterpolating to isus time values...
Interpolating ctd2 temperature...
Interpolating ctd2 salinity...
5 NaNs found in bbpBlue.  Interpolating anyway.
5 NaNs found in bbpRed.  Interpolating anyway.
3 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 1124 NaN values in array of lon that is 64090 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 62966 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 62966 are not equal to number of Lat lon points = 64090
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.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00.txt
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00.txt...
Copied to /mbari/AUVCTD/surveys/2017/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2017/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing netCDF file ...
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00.nc...
Copied to /mbari/AUVCTD/surveys/2017/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2017/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_304_00_304_00.mat...
Copied to /mbari/AUVCTD/surveys/2017/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
permalink_url.sh http://dods.mbari.org/cgi-bin/nph-nc/data/auvctd/surveys/2017/netcdf/Dorado389_2017_304_00_304_00.nc
 
 
*************************************************************************
Composing email to send to auvctd@listserver.mbari.org ...
!mail -s "Survey Dorado389_2017_304_00_304_00 processed" auvctd@listserver.mbari.org < mail_Dorado389_2017_304_00_304_00.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017.304.00.mat
Processing time: 257 seconds