Execution of AUVprocess_main version 1.88 at 2022-04-27T17:34:57Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2022, ['110.13'], '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: 2022.110.13
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/
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/2022/2022110/2022.110.13/navigation.nc')
Creating vector time with 354955 elements.
Creating vector mPos_x with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mPos_y with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mDepth with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mGpsNorth with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mGpsEast with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mGpsValid with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mPhi with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mTheta with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mPsi with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mOmega_x with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mOmega_y with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mOmega_z with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mPsaRange with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mAltitude with 354955 elements.
Creating vector time with 354955 elements.
Creating vector multibeamAltitude with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mDvlAltitude with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mEchoAltitude with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mEchoHorizRange with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mEchoAltitudeLast with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mEchoHorizRangeLast with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mEchoNumOfPings with 354955 elements.
Creating vector time with 354955 elements.
Creating vector nadirCnts with 354955 elements.
Creating vector time with 354955 elements.
Creating vector obstacleCnts with 354955 elements.
Creating vector time with 354955 elements.
Creating vector nGoodNadirBeams with 354955 elements.
Creating vector time with 354955 elements.
Creating vector medianNadirBeamNo with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mWaterSpeed with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mDvlValid with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mDvlNewData with 354955 elements.
Creating vector time with 354955 elements.
Creating vector mDeltaT with 354955 elements.
Creating vector time with 354955 elements.
Creating vector nfix with 354955 elements.
Creating vector time with 354955 elements.
Creating vector efix with 354955 elements.
Creating vector time with 354955 elements.
Creating vector filter_north with 354955 elements.
Creating vector time with 354955 elements.
Creating vector filter_east with 354955 elements.
Creating vector time with 354955 elements.
Creating vector filter_depth with 354955 elements.
Creating vector time with 354955 elements.
Creating vector north_current with 354955 elements.
Creating vector time with 354955 elements.
Creating vector east_current with 354955 elements.
Creating vector time with 354955 elements.
Creating vector speed_bias with 354955 elements.
Creating vector time with 354955 elements.
Creating vector heading_bias with 354955 elements.
Creating vector time with 354955 elements.
Creating vector latitude with 354955 elements.
Creating vector time with 354955 elements.
Creating vector longitude with 354955 elements.
Creating vector time with 354955 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/navigation.nc');
processNav(): median of positive valued depths = 28.5372
processNav(): Finding depths less than 285.3719 and times > 0
processNav(): length(Nav.depth) = 354955
processNav(): length(gindx)     = 354955
 
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/2022/2022110/2022.110.13/gps.nc')
Creating vector time with 17297 elements.
Creating vector hours with 17297 elements.
Creating vector time with 17297 elements.
Creating vector minutes with 17297 elements.
Creating vector time with 17297 elements.
Creating vector seconds with 17297 elements.
Creating vector time with 17297 elements.
Creating vector centiSeconds with 17297 elements.
Creating vector time with 17297 elements.
Creating vector latitude with 17297 elements.
Creating vector time with 17297 elements.
Creating vector longitude with 17297 elements.
Creating vector time with 17297 elements.
Creating vector quality with 17297 elements.
Creating vector time with 17297 elements.
Creating vector numberOfSatellites with 17297 elements.
Creating vector time with 17297 elements.
Creating vector hdop with 17297 elements.
Creating vector time with 17297 elements.
Creating vector antennaHeight with 17297 elements.
Creating vector time with 17297 elements.
Creating vector geoHeight with 17297 elements.
Creating vector time with 17297 elements.
Creating vector dgpsDataAge with 17297 elements.
Creating vector time with 17297 elements.
Creating vector dgpsRSID with 17297 elements.
Creating vector time with 17297 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/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/2022/2022110/2022.110.13/parosci.nc')
Creating vector time with 706874 elements.
Creating vector depth with 706874 elements.
Creating vector time with 706874 elements.
Creating vector temp with 706874 elements.
Creating vector time with 706874 elements.
Creating vector pressure with 706874 elements.
Creating vector time with 706874 elements.
Creating vector temp_period with 706874 elements.
Creating vector time with 706874 elements.
Creating vector pres_period with 706874 elements.
Creating vector time with 706874 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.35506 max(Depth.data) = 202.4502
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.35506 max(Depth.data) = 202.4502
 
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/2022/2022110/2022.110.13/hydroscatlog.nc')
Creating vector time with 283930 elements.
Creating vector Seconds with 283930 elements.
Creating vector time with 283930 elements.
Creating vector HundrethsOfSeconds with 283930 elements.
Creating vector time with 283930 elements.
Creating vector Snorm1 with 283930 elements.
Creating vector time with 283930 elements.
Creating vector Snorm2 with 283930 elements.
Creating vector time with 283930 elements.
Creating vector Snorm3 with 283930 elements.
Creating vector time with 283930 elements.
Creating vector Gain_Status_1 with 283930 elements.
Creating vector time with 283930 elements.
Creating vector Gain_Status_2 with 283930 elements.
Creating vector time with 283930 elements.
Creating vector Gain_Status_3 with 283930 elements.
Creating vector time with 283930 elements.
Creating vector RawDepthValue with 283930 elements.
Creating vector time with 283930 elements.
Creating vector RawTempValue with 283930 elements.
Creating vector time with 283930 elements.
Creating vector Temperature with 283930 elements.
Creating vector time with 283930 elements.
Creating vector ErrorValue with 283930 elements.
Creating vector time with 283930 elements.
Creating vector bb470 with 283930 elements.
Creating vector time with 283930 elements.
Creating vector bb676 with 283930 elements.
Creating vector time with 283930 elements.
Creating vector fl676u with 283930 elements.
Creating vector time with 283930 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/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/2022/2022110/2022.110.13/ctdDriver.nc')
Creating vector time with 284054 elements.
Creating vector conductivity with 284054 elements.
Creating vector time with 284054 elements.
Creating vector temperature with 284054 elements.
Creating vector time with 284054 elements.
Creating vector cond_frequency with 284054 elements.
Creating vector time with 284054 elements.
Creating vector temp_frequency with 284054 elements.
Creating vector time with 284054 elements.
Creating vector spare with 284054 elements.
Creating vector time with 284054 elements.
Creating vector humidity with 284054 elements.
Creating vector time with 284054 elements.
Creating vector flow1 with 284054 elements.
Creating vector time with 284054 elements.
Creating vector CDOM with 284054 elements.
Creating vector time with 284054 elements.
Creating vector dissolvedO2 with 284054 elements.
Creating vector time with 284054 elements.
Creating vector salinity with 284054 elements.
Creating vector time with 284054 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/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/2022/2022110/2022.110.13/ctdDriver2.nc')
Creating vector time with 284053 elements.
Creating vector conductivity with 284053 elements.
Creating vector time with 284053 elements.
Creating vector temperature with 284053 elements.
Creating vector time with 284053 elements.
Creating vector cond_frequency with 284053 elements.
Creating vector time with 284053 elements.
Creating vector temp_frequency with 284053 elements.
Creating vector time with 284053 elements.
Creating vector flow2 with 284053 elements.
Creating vector time with 284053 elements.
Creating vector par with 284053 elements.
Creating vector time with 284053 elements.
Creating vector spare with 284053 elements.
Creating vector time with 284053 elements.
Creating vector salinity with 284053 elements.
Creating vector time with 284053 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/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/2022/2022110/2022.110.13/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/2022/2022110/2022.110.13/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/2022/2022110/2022.110.13/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/2022/2022110/2022.110.13/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/2022/2022110/2022.110.13/biolume.nc')
Creating vector time with 69827 elements.
Creating vector rrr with 69827 elements.
Creating vector time with 69827 elements.
Creating vector cal_striing with 69827 elements.
Creating vector time with 69827 elements.
Creating vector avg_biolume with 69827 elements.
Creating vector time with 69827 elements.
Creating vector pump with 69827 elements.
Creating vector time with 69827 elements.
Creating vector system_voltage with 69827 elements.
Creating vector time with 69827 elements.
Creating vector flow with 69827 elements.
Creating vector time with 69827 elements.
Creating vector HV with 69827 elements.
Creating vector time with 69827 elements.
Creating vector reserved with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_0 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_1 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_2 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_3 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_4 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_5 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_6 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_7 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_8 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_9 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_10 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_11 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_12 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_13 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_14 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_15 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_16 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_17 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_18 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_19 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_20 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_21 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_22 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_23 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_24 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_25 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_26 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_27 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_28 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_29 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_30 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_31 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_32 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_33 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_34 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_35 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_36 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_37 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_38 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_39 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_40 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_41 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_42 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_43 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_44 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_45 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_46 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_47 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_48 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_49 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_50 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_51 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_52 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_53 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_54 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_55 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_56 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_57 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_58 with 69827 elements.
Creating vector time with 69827 elements.
Creating vector raw_59 with 69827 elements.
Creating vector time with 69827 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/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/2022/2022110/2022.110.13/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (6764 x 994) with 6723416 elements.
Creating vector time with 6764 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (6764 x 994) with 6723416 elements.
Creating vector time with 6764 elements.
Creating vector bin with 994 elements.
Creating matrix countList (6764 x 994) with 6723416 elements.
Creating vector time with 6764 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 6764 elements.
Creating vector time with 6764 elements.
Creating vector transCount with 6764 elements.
Creating vector time with 6764 elements.
Creating vector nonTransCount with 6764 elements.
Creating vector time with 6764 elements.
Creating vector ai_mean with 6764 elements.
Creating vector time with 6764 elements.
Creating vector ai_min with 6764 elements.
Creating vector time with 6764 elements.
Creating vector ai_max with 6764 elements.
Creating vector time with 6764 elements.
Creating vector ai_std with 6764 elements.
Creating vector time with 6764 elements.
Creating vector esd_mean with 6764 elements.
Creating vector time with 6764 elements.
Creating vector esd_min with 6764 elements.
Creating vector time with 6764 elements.
Creating vector esd_max with 6764 elements.
Creating vector time with 6764 elements.
Creating vector esd_std with 6764 elements.
Creating vector time with 6764 elements.
Creating vector countSum with 6764 elements.
Creating vector time with 6764 elements.
Creating vector snapshot with 6764 elements.
Creating vector time with 6764 elements.
Creating vector threshold with 6764 elements.
Creating vector time with 6764 elements.
Creating vector sampleCount with 6764 elements.
Creating vector time with 6764 elements.
Creating vector flowCount with 6764 elements.
Creating vector time with 6764 elements.
Creating vector flowTime with 6764 elements.
Creating vector time with 6764 elements.
Creating vector bufferStatus with 6764 elements.
Creating vector time with 6764 elements.
Creating vector laserLevel with 6764 elements.
Creating vector time with 6764 elements.
Creating vector counter with 6764 elements.
Creating vector time with 6764 elements.
Creating vector counterPeriod with 6764 elements.
Creating vector time with 6764 elements.
Creating vector laserControl with 6764 elements.
Creating vector time with 6764 elements.
Creating vector countUnknownFrameCharacter with 6764 elements.
Creating vector time with 6764 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 6764 elements.
Creating vector time with 6764 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 6764 elements.
Creating vector time with 6764 elements.
Creating vector flowSpeed with 6764 elements.
Creating vector time with 6764 elements.
Creating vector countShortLFrameError with 6764 elements.
Creating vector time with 6764 elements.
Creating vector countGarbledLFrame with 6764 elements.
Creating vector time with 6764 elements.
Creating vector cFrameEsecs with 6764 elements.
Creating vector time with 6764 elements.
Creating vector correctedSampleCountList with 6764 elements.
Creating vector time with 6764 elements.
Creating vector time with 6764 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022110/2022.110.13/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022.110.13.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_2022.110.13.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 38 segments.
*** WARNING: no data in dvlSegSurfLat for segment 26.  Continuing to next segment
[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_110_13_110_13_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_110_13_110_13.mat
Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_110_13_110_13.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 = 434 Gridding with nix = 1302, 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 329440 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 329440 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 153155 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 04/20/2022 11:30  to 04/21/2022 09:30 

swr =

  906.6203
  996.2000
  999.5000
  936.1286
  788.0690
  579.7808
  382.6891
  102.8790
   16.0198
    6.1280
    6.0806
    6.0806
    6.2023
    6.5752
    6.4667
    6.3248
    6.6333
    6.3838
    6.1527
   23.8352
   57.5349
  167.1381
  323.6445

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_110_13_110_13_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2022110_GulperTimes.txt && touch ../results/2022110_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/2022/2022110/2022.110.13/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2022/2022110/2022.110.13/syslog -startEsecs 1650485891.8741 -surveyName Dorado389_2022_110_13_110_13 >> ../results/2022110_GulperTimes.txt
Executing: removeGulpDups.py ../results/2022110_GulperTimes.txt
Bottle: 0 Time: 1650488358.8751 Depth: 149.9966 Dist: 1.9658
Bottle: 1 Time: 1650488488.2662 Depth: 99.9384 Dist: 2.101
Bottle: 2 Time: 1650488560.4713 Depth: 59.9178 Dist: 2.186
Bottle: 3 Time: 1650488669.0738 Depth: 19.9289 Dist: 2.3053
Bottle: 4 Time: 1650488718.6704 Depth: 4.9323 Dist: 2.3554
Bottle: 5 Time: 1650492372.6701 Depth: 5.0588 Dist: 6.7015
Bottle: 6 Time: 1650495315.0686 Depth: 5.0008 Dist: 10.5618
Bottle: 7 Time: 1650498533.0681 Depth: 5.0501 Dist: 14.5992
Bottle: 8 Time: 1650502088.0746 Depth: 5.0528 Dist: 18.8292
Bottle: 9 Time: 1650505612.4732 Depth: 5.0245 Dist: 23.1361
Bottle: 10 Time: 1650509004.8707 Depth: 5.0504 Dist: 27.1586
Bottle: 11 Time: 1650512527.8694 Depth: 5.0197 Dist: 31.317
Bottle: 12 Time: 1650515959.6743 Depth: 5.0103 Dist: 35.3579
Bottle: 13 Time: 1650520752.186 Depth: 5.0993 Dist: 40.9923
Bottle: 14 Time: 1650523968.4757 Depth: 5.0142 Dist: 45.3121
Bottle: 15 Time: 1650527343.6745 Depth: 5.0013 Dist: 49.6544
Bottle: 16 Time: 1650530740.8717 Depth: 5.0147 Dist: 53.8473
Bottle: 17 Time: 1650534232.4725 Depth: 5.0774 Dist: 57.7354
Bottle: 18 Time: 1650537804.2679 Depth: -0.090366 Dist: 61.8755
Bottle: 19 Time: 1650541083.2732 Depth: 5.0658 Dist: 65.6841
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_110_13_110_13_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_2022_110_13_110_13_2column.png
Elapsed time to save image: 15 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_2022_110_13_110_13_biolume.png
Elapsed time to save image: 59 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_2022_110_13_110_13_lopc.png
Elapsed time to save image: 15 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_110_13_110_13_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_110_13_110_13_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_110_13_110_13_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_110_13_110_13_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_110_13_110_13_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_110_13_110_13_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_110_13_110_13_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_110_13_110_13_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) = 2022-04-20T20:18:11Z
gmtstr(tend) = 2022-04-21T16:01:22Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
5 NaNs found in bbpRed.  Interpolating anyway.
1 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_2022_110_13_110_13_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_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.
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_Nitrate.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_110_13_110_13_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_110_13_110_13.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_110_13_110_13.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_110_13_110_13_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_110_13_110_13.mat ...
Iterpolating to 2 second increments between Nav time bounds...
gmtstr(tstart) = 2022-04-20T20:18:11Z
gmtstr(tend) = 2022-04-21T16:01:22Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
5 NaNs found in bbpRed.  Interpolating anyway.
1 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 1791 NaN values in array of lon that is 35496 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 33705 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 33705 are not equal to number of Lat lon points = 35496
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_110_13_110_13.txt
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_110_13_110_13_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_110_13_110_13.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_110_13_110_13_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_110_13_110_13.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_110_13_110_13_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_110_13_110_13.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_110_13_110_13.nc
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2022_110_13_110_13 processed" mccann@mbari.org < mail_Dorado389_2022_110_13_110_13.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022.110.13.mat
Processing time: 286 seconds