Execution of AUVprocess_main version 1.88 at 2022-03-22T21:33:41Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2022, ['075.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1')
 
*************************************************************************
Processing data from SSDS via DODS server
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2022.075.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/
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/2022/2022075/2022.075.00/navigation.nc')
Creating vector time with 346565 elements.
Creating vector mPos_x with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mPos_y with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mDepth with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mGpsNorth with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mGpsEast with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mGpsValid with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mPhi with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mTheta with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mPsi with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mOmega_x with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mOmega_y with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mOmega_z with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mPsaRange with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mAltitude with 346565 elements.
Creating vector time with 346565 elements.
Creating vector multibeamAltitude with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mDvlAltitude with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mEchoAltitude with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mEchoHorizRange with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mEchoAltitudeLast with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mEchoHorizRangeLast with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mEchoNumOfPings with 346565 elements.
Creating vector time with 346565 elements.
Creating vector nadirCnts with 346565 elements.
Creating vector time with 346565 elements.
Creating vector obstacleCnts with 346565 elements.
Creating vector time with 346565 elements.
Creating vector nGoodNadirBeams with 346565 elements.
Creating vector time with 346565 elements.
Creating vector medianNadirBeamNo with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mWaterSpeed with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mDvlValid with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mDvlNewData with 346565 elements.
Creating vector time with 346565 elements.
Creating vector mDeltaT with 346565 elements.
Creating vector time with 346565 elements.
Creating vector nfix with 346565 elements.
Creating vector time with 346565 elements.
Creating vector efix with 346565 elements.
Creating vector time with 346565 elements.
Creating vector filter_north with 346565 elements.
Creating vector time with 346565 elements.
Creating vector filter_east with 346565 elements.
Creating vector time with 346565 elements.
Creating vector filter_depth with 346565 elements.
Creating vector time with 346565 elements.
Creating vector north_current with 346565 elements.
Creating vector time with 346565 elements.
Creating vector east_current with 346565 elements.
Creating vector time with 346565 elements.
Creating vector speed_bias with 346565 elements.
Creating vector time with 346565 elements.
Creating vector heading_bias with 346565 elements.
Creating vector time with 346565 elements.
Creating vector latitude with 346565 elements.
Creating vector time with 346565 elements.
Creating vector longitude with 346565 elements.
Creating vector time with 346565 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/navigation.nc');
processNav(): median of positive valued depths = 29.0547
processNav(): Finding depths less than 290.5469 and times > 0
processNav(): length(Nav.depth) = 346565
processNav(): length(gindx)     = 346565
 
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/2022/2022075/2022.075.00/gps.nc')
Creating vector time with 13897 elements.
Creating vector hours with 13897 elements.
Creating vector time with 13897 elements.
Creating vector minutes with 13897 elements.
Creating vector time with 13897 elements.
Creating vector seconds with 13897 elements.
Creating vector time with 13897 elements.
Creating vector centiSeconds with 13897 elements.
Creating vector time with 13897 elements.
Creating vector latitude with 13897 elements.
Creating vector time with 13897 elements.
Creating vector longitude with 13897 elements.
Creating vector time with 13897 elements.
Creating vector quality with 13897 elements.
Creating vector time with 13897 elements.
Creating vector numberOfSatellites with 13897 elements.
Creating vector time with 13897 elements.
Creating vector hdop with 13897 elements.
Creating vector time with 13897 elements.
Creating vector antennaHeight with 13897 elements.
Creating vector time with 13897 elements.
Creating vector geoHeight with 13897 elements.
Creating vector time with 13897 elements.
Creating vector dgpsDataAge with 13897 elements.
Creating vector time with 13897 elements.
Creating vector dgpsRSID with 13897 elements.
Creating vector time with 13897 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/gps.nc');
 
Processing depth data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/parosci.nc')
Creating vector time with 690162 elements.
Creating vector depth with 690162 elements.
Creating vector time with 690162 elements.
Creating vector temp with 690162 elements.
Creating vector time with 690162 elements.
Creating vector pressure with 690162 elements.
Creating vector time with 690162 elements.
Creating vector temp_period with 690162 elements.
Creating vector time with 690162 elements.
Creating vector pres_period with 690162 elements.
Creating vector time with 690162 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.32375 max(Depth.data) = 202.3691
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.32375 max(Depth.data) = 202.3691
 
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/2022/2022075/2022.075.00/hydroscatlog.nc')
Creating vector time with 277249 elements.
Creating vector Seconds with 277249 elements.
Creating vector time with 277249 elements.
Creating vector HundrethsOfSeconds with 277249 elements.
Creating vector time with 277249 elements.
Creating vector Snorm1 with 277249 elements.
Creating vector time with 277249 elements.
Creating vector Snorm2 with 277249 elements.
Creating vector time with 277249 elements.
Creating vector Snorm3 with 277249 elements.
Creating vector time with 277249 elements.
Creating vector Gain_Status_1 with 277249 elements.
Creating vector time with 277249 elements.
Creating vector Gain_Status_2 with 277249 elements.
Creating vector time with 277249 elements.
Creating vector Gain_Status_3 with 277249 elements.
Creating vector time with 277249 elements.
Creating vector RawDepthValue with 277249 elements.
Creating vector time with 277249 elements.
Creating vector RawTempValue with 277249 elements.
Creating vector time with 277249 elements.
Creating vector Temperature with 277249 elements.
Creating vector time with 277249 elements.
Creating vector ErrorValue with 277249 elements.
Creating vector time with 277249 elements.
Creating vector bb470 with 277249 elements.
Creating vector time with 277249 elements.
Creating vector bb676 with 277249 elements.
Creating vector time with 277249 elements.
Creating vector fl676u with 277249 elements.
Creating vector time with 277249 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/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/2022/2022075/2022.075.00/ctdDriver.nc')
Creating vector time with 277302 elements.
Creating vector conductivity with 277302 elements.
Creating vector time with 277302 elements.
Creating vector temperature with 277302 elements.
Creating vector time with 277302 elements.
Creating vector cond_frequency with 277302 elements.
Creating vector time with 277302 elements.
Creating vector temp_frequency with 277302 elements.
Creating vector time with 277302 elements.
Creating vector spare with 277302 elements.
Creating vector time with 277302 elements.
Creating vector humidity with 277302 elements.
Creating vector time with 277302 elements.
Creating vector flow1 with 277302 elements.
Creating vector time with 277302 elements.
Creating vector CDOM with 277302 elements.
Creating vector time with 277302 elements.
Creating vector dissolvedO2 with 277302 elements.
Creating vector time with 277302 elements.
Creating vector salinity with 277302 elements.
Creating vector time with 277302 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/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/2022/2022075/2022.075.00/ctdDriver2.nc')
Creating vector time with 277174 elements.
Creating vector conductivity with 277174 elements.
Creating vector time with 277174 elements.
Creating vector temperature with 277174 elements.
Creating vector time with 277174 elements.
Creating vector cond_frequency with 277174 elements.
Creating vector time with 277174 elements.
Creating vector temp_frequency with 277174 elements.
Creating vector time with 277174 elements.
Creating vector flow2 with 277174 elements.
Creating vector time with 277174 elements.
Creating vector par with 277174 elements.
Creating vector time with 277174 elements.
Creating vector spare with 277174 elements.
Creating vector time with 277174 elements.
Creating vector salinity with 277174 elements.
Creating vector time with 277174 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/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/2022/2022075/2022.075.00/isuslog.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/isuslog.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/isuslog.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/isuslog.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


*** Setting ISUS structure to NaN values.
 
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/2022/2022075/2022.075.00/biolume.nc')
Creating vector time with 68178 elements.
Creating vector rrr with 68178 elements.
Creating vector time with 68178 elements.
Creating vector cal_striing with 68178 elements.
Creating vector time with 68178 elements.
Creating vector avg_biolume with 68178 elements.
Creating vector time with 68178 elements.
Creating vector pump with 68178 elements.
Creating vector time with 68178 elements.
Creating vector system_voltage with 68178 elements.
Creating vector time with 68178 elements.
Creating vector flow with 68178 elements.
Creating vector time with 68178 elements.
Creating vector HV with 68178 elements.
Creating vector time with 68178 elements.
Creating vector reserved with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_0 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_1 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_2 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_3 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_4 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_5 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_6 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_7 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_8 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_9 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_10 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_11 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_12 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_13 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_14 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_15 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_16 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_17 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_18 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_19 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_20 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_21 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_22 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_23 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_24 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_25 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_26 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_27 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_28 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_29 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_30 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_31 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_32 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_33 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_34 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_35 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_36 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_37 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_38 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_39 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_40 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_41 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_42 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_43 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_44 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_45 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_46 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_47 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_48 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_49 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_50 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_51 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_52 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_53 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_54 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_55 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_56 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_57 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_58 with 68178 elements.
Creating vector time with 68178 elements.
Creating vector raw_59 with 68178 elements.
Creating vector time with 68178 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/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/2022/2022075/2022.075.00/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (6604 x 994) with 6564376 elements.
Creating vector time with 6604 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (6604 x 994) with 6564376 elements.
Creating vector time with 6604 elements.
Creating vector bin with 994 elements.
Creating matrix countList (6604 x 994) with 6564376 elements.
Creating vector time with 6604 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 6604 elements.
Creating vector time with 6604 elements.
Creating vector transCount with 6604 elements.
Creating vector time with 6604 elements.
Creating vector nonTransCount with 6604 elements.
Creating vector time with 6604 elements.
Creating vector ai_mean with 6604 elements.
Creating vector time with 6604 elements.
Creating vector ai_min with 6604 elements.
Creating vector time with 6604 elements.
Creating vector ai_max with 6604 elements.
Creating vector time with 6604 elements.
Creating vector ai_std with 6604 elements.
Creating vector time with 6604 elements.
Creating vector esd_mean with 6604 elements.
Creating vector time with 6604 elements.
Creating vector esd_min with 6604 elements.
Creating vector time with 6604 elements.
Creating vector esd_max with 6604 elements.
Creating vector time with 6604 elements.
Creating vector esd_std with 6604 elements.
Creating vector time with 6604 elements.
Creating vector countSum with 6604 elements.
Creating vector time with 6604 elements.
Creating vector snapshot with 6604 elements.
Creating vector time with 6604 elements.
Creating vector threshold with 6604 elements.
Creating vector time with 6604 elements.
Creating vector sampleCount with 6604 elements.
Creating vector time with 6604 elements.
Creating vector flowCount with 6604 elements.
Creating vector time with 6604 elements.
Creating vector flowTime with 6604 elements.
Creating vector time with 6604 elements.
Creating vector bufferStatus with 6604 elements.
Creating vector time with 6604 elements.
Creating vector laserLevel with 6604 elements.
Creating vector time with 6604 elements.
Creating vector counter with 6604 elements.
Creating vector time with 6604 elements.
Creating vector counterPeriod with 6604 elements.
Creating vector time with 6604 elements.
Creating vector laserControl with 6604 elements.
Creating vector time with 6604 elements.
Creating vector countUnknownFrameCharacter with 6604 elements.
Creating vector time with 6604 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 6604 elements.
Creating vector time with 6604 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 6604 elements.
Creating vector time with 6604 elements.
Creating vector flowSpeed with 6604 elements.
Creating vector time with 6604 elements.
Creating vector countShortLFrameError with 6604 elements.
Creating vector time with 6604 elements.
Creating vector countGarbledLFrame with 6604 elements.
Creating vector time with 6604 elements.
Creating vector cFrameEsecs with 6604 elements.
Creating vector time with 6604 elements.
Creating vector correctedSampleCountList with 6604 elements.
Creating vector time with 6604 elements.
Creating vector time with 6604 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022075/2022.075.00/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022.075.00.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_2022.075.00.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 38 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_2022_075_00_075_00_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_00.mat
Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_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 = 422 Gridding with nix = 1266, 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
Only one good point - NaNing the gN array.
   BL
   BLflow
   LOPC
     count
     transCount
     nonTransCount
     LCcount
 
Masking and filtering with median filter of size 5...
  cvarname = gT
  cvarname = gS
  cvarname = gO
  cvarname = gN
No valid data for 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 341483 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 341483 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.
*** 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 = 26372.8752 since 1/1/1950
Looking for end   days = 26373.6774
sIndx = 
eIndx = 
Met data goes from 20017.6042 to 26097.7292
No SWR data loaded from URL.
Executing: /bin/rm -f ../results/2022075_GulperTimes.txt && touch ../results/2022075_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/2022/2022075/2022.075.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2022/2022075/2022.075.00/syslog -startEsecs 1647464414.3306 -surveyName Dorado389_2022_075_00_075_00 >> ../results/2022075_GulperTimes.txt
Executing: removeGulpDups.py ../results/2022075_GulperTimes.txt
Bottle: 0 Time: 1647468193.9317 Depth: 149.9189 Dist: 3.8398
Bottle: 1 Time: 1647468321.5229 Depth: 99.9945 Dist: 3.9713
Bottle: 2 Time: 1647468427.1257 Depth: 59.9841 Dist: 4.0831
Bottle: 3 Time: 1647468533.3284 Depth: 19.9126 Dist: 4.1864
Bottle: 4 Time: 1647468582.3251 Depth: 4.95 Dist: 4.2334
Bottle: 5 Time: 1647472419.3322 Depth: 5.053 Dist: 8.6427
Bottle: 6 Time: 1647475525.6694 Depth: 5.137 Dist: 12.629
Bottle: 7 Time: 1647478547.7324 Depth: 5.0768 Dist: 16.615
Bottle: 8 Time: 1647481786.7305 Depth: 5.0316 Dist: 20.7553
Bottle: 9 Time: 1647485399.523 Depth: 5.036 Dist: 24.991
Bottle: 10 Time: 1647489257.9287 Depth: 5.0438 Dist: 29.41
Bottle: 11 Time: 1647492865.3316 Depth: 5.0753 Dist: 33.4688
Bottle: 12 Time: 1647496624.924 Depth: 5.0378 Dist: 37.6729
Bottle: 13 Time: 1647502432.3262 Depth: 5.0649 Dist: 44.0334
Bottle: 14 Time: 1647506140.1322 Depth: -0.037729 Dist: 48.4417
Bottle: 15 Time: 1647509770.5235 Depth: -0.033882 Dist: 52.813
Bottle: 16 Time: 1647513374.7266 Depth: 4.4876 Dist: 57.0188
Bottle: 17 Time: 1647516530.9304 Depth: 5.0895 Dist: 60.7927
Bottle: 18 Time: 1647519862.1322 Depth: 4.1687 Dist: 64.867
Bottle: 19 Time: 1647523022.5257 Depth: 5.0604 Dist: 68.7274
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_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
Did not add swr plot to the image.
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_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
SWR image not added to the plot.
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_00_biolume.png
Elapsed time to save image: 43 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.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_00_lopc.png
Elapsed time to save image: 13 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_2022_075_00_075_00_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_00_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_00_2column.png...
Copied to /mbari/AUVCTD/surveys/2022/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_2022_075_00_075_00_biolume.png...
Copied to /mbari/AUVCTD/surveys/2022/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_2022_075_00_075_00_lopc.png...
Copied to /mbari/AUVCTD/surveys/2022/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_2022_075_00_075_00_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2022/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_2022_075_00_075_00_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2022/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_2022_075_00_075_00_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2022/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to 2 second increments between Nav time bounds...
gmtstr(tstart) = 2022-03-16T21:00:14Z
gmtstr(tend) = 2022-03-17T16:15:27Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
22 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_00_decim.nc...
Copied to /mbari/AUVCTD/surveys/2022/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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2022/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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2022/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);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Nitrate.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2022/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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2022/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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2022/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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2022/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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2022/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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2022/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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_075_00_075_00_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2022/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
Creating Dorado389_2022_075_00_075_00.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_00.kml...
Copied to /mbari/AUVCTD/surveys/2022/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_2022_075_00_075_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_2022_075_00_075_00.mat ...
Iterpolating to 2 second increments between Nav time bounds...
gmtstr(tstart) = 2022-03-16T21:00:14Z
gmtstr(tend) = 2022-03-17T16:15:27Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
22 NaNs found in bbpRed.  Interpolating anyway.
Encountered 509 NaN values in array of lon that is 34657 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 34148 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 34148 are not equal to number of Lat lon points = 34657
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_2022_075_00_075_00.txt
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_00_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_075_00_075_00.txt...
Copied to /mbari/AUVCTD/surveys/2022/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_2022_075_00_075_00_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2022/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_2022_075_00_075_00.nc...
Copied to /mbari/AUVCTD/surveys/2022/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_2022_075_00_075_00_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2022/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_2022_075_00_075_00.mat...
Copied to /mbari/AUVCTD/surveys/2022/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/2022/netcdf/Dorado389_2022_075_00_075_00.nc
 
 
*************************************************************************
Composing email to send to auvctd@listserver.mbari.org ...
!mail -s "Survey Dorado389_2022_075_00_075_00 processed" auvctd@listserver.mbari.org < mail_Dorado389_2022_075_00_075_00.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022.075.00.mat
Processing time: 253 seconds