Execution of AUVprocess_main version 1.88 at 2022-06-02T17:22:06Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2022, ['138.00'], '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: 2022.138.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/
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/2022/2022138/2022.138.00/navigation.nc')
Creating vector time with 341965 elements.
Creating vector mPos_x with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mPos_y with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mDepth with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mGpsNorth with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mGpsEast with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mGpsValid with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mPhi with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mTheta with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mPsi with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mOmega_x with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mOmega_y with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mOmega_z with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mPsaRange with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mAltitude with 341965 elements.
Creating vector time with 341965 elements.
Creating vector multibeamAltitude with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mDvlAltitude with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mEchoAltitude with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mEchoHorizRange with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mEchoAltitudeLast with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mEchoHorizRangeLast with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mEchoNumOfPings with 341965 elements.
Creating vector time with 341965 elements.
Creating vector nadirCnts with 341965 elements.
Creating vector time with 341965 elements.
Creating vector obstacleCnts with 341965 elements.
Creating vector time with 341965 elements.
Creating vector nGoodNadirBeams with 341965 elements.
Creating vector time with 341965 elements.
Creating vector medianNadirBeamNo with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mWaterSpeed with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mDvlValid with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mDvlNewData with 341965 elements.
Creating vector time with 341965 elements.
Creating vector mDeltaT with 341965 elements.
Creating vector time with 341965 elements.
Creating vector nfix with 341965 elements.
Creating vector time with 341965 elements.
Creating vector efix with 341965 elements.
Creating vector time with 341965 elements.
Creating vector filter_north with 341965 elements.
Creating vector time with 341965 elements.
Creating vector filter_east with 341965 elements.
Creating vector time with 341965 elements.
Creating vector filter_depth with 341965 elements.
Creating vector time with 341965 elements.
Creating vector north_current with 341965 elements.
Creating vector time with 341965 elements.
Creating vector east_current with 341965 elements.
Creating vector time with 341965 elements.
Creating vector speed_bias with 341965 elements.
Creating vector time with 341965 elements.
Creating vector heading_bias with 341965 elements.
Creating vector time with 341965 elements.
Creating vector latitude with 341965 elements.
Creating vector time with 341965 elements.
Creating vector longitude with 341965 elements.
Creating vector time with 341965 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/navigation.nc');
processNav(): median of positive valued depths = 28.7801
processNav(): Finding depths less than 287.8014 and times > 0
processNav(): length(Nav.depth) = 341965
processNav(): length(gindx)     = 341965
 
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/2022/2022138/2022.138.00/gps.nc')
Creating vector time with 13808 elements.
Creating vector hours with 13808 elements.
Creating vector time with 13808 elements.
Creating vector minutes with 13808 elements.
Creating vector time with 13808 elements.
Creating vector seconds with 13808 elements.
Creating vector time with 13808 elements.
Creating vector centiSeconds with 13808 elements.
Creating vector time with 13808 elements.
Creating vector latitude with 13808 elements.
Creating vector time with 13808 elements.
Creating vector longitude with 13808 elements.
Creating vector time with 13808 elements.
Creating vector quality with 13808 elements.
Creating vector time with 13808 elements.
Creating vector numberOfSatellites with 13808 elements.
Creating vector time with 13808 elements.
Creating vector hdop with 13808 elements.
Creating vector time with 13808 elements.
Creating vector antennaHeight with 13808 elements.
Creating vector time with 13808 elements.
Creating vector geoHeight with 13808 elements.
Creating vector time with 13808 elements.
Creating vector dgpsDataAge with 13808 elements.
Creating vector time with 13808 elements.
Creating vector dgpsRSID with 13808 elements.
Creating vector time with 13808 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/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/2022/2022138/2022.138.00/parosci.nc')
Creating vector time with 681030 elements.
Creating vector depth with 681030 elements.
Creating vector time with 681030 elements.
Creating vector temp with 681030 elements.
Creating vector time with 681030 elements.
Creating vector pressure with 681030 elements.
Creating vector time with 681030 elements.
Creating vector temp_period with 681030 elements.
Creating vector time with 681030 elements.
Creating vector pres_period with 681030 elements.
Creating vector time with 681030 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.37016 max(Depth.data) = 202.7191
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.37016 max(Depth.data) = 202.7191
 
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/2022/2022138/2022.138.00/hydroscatlog.nc')
Creating vector time with 273562 elements.
Creating vector Seconds with 273562 elements.
Creating vector time with 273562 elements.
Creating vector HundrethsOfSeconds with 273562 elements.
Creating vector time with 273562 elements.
Creating vector Snorm1 with 273562 elements.
Creating vector time with 273562 elements.
Creating vector Snorm2 with 273562 elements.
Creating vector time with 273562 elements.
Creating vector Snorm3 with 273562 elements.
Creating vector time with 273562 elements.
Creating vector Gain_Status_1 with 273562 elements.
Creating vector time with 273562 elements.
Creating vector Gain_Status_2 with 273562 elements.
Creating vector time with 273562 elements.
Creating vector Gain_Status_3 with 273562 elements.
Creating vector time with 273562 elements.
Creating vector RawDepthValue with 273562 elements.
Creating vector time with 273562 elements.
Creating vector RawTempValue with 273562 elements.
Creating vector time with 273562 elements.
Creating vector Temperature with 273562 elements.
Creating vector time with 273562 elements.
Creating vector ErrorValue with 273562 elements.
Creating vector time with 273562 elements.
Creating vector bb470 with 273562 elements.
Creating vector time with 273562 elements.
Creating vector bb676 with 273562 elements.
Creating vector time with 273562 elements.
Creating vector fl676u with 273562 elements.
Creating vector time with 273562 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/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/2022/2022138/2022.138.00/ctdDriver.nc')
Creating vector time with 273629 elements.
Creating vector conductivity with 273629 elements.
Creating vector time with 273629 elements.
Creating vector temperature with 273629 elements.
Creating vector time with 273629 elements.
Creating vector cond_frequency with 273629 elements.
Creating vector time with 273629 elements.
Creating vector temp_frequency with 273629 elements.
Creating vector time with 273629 elements.
Creating vector spare with 273629 elements.
Creating vector time with 273629 elements.
Creating vector humidity with 273629 elements.
Creating vector time with 273629 elements.
Creating vector flow1 with 273629 elements.
Creating vector time with 273629 elements.
Creating vector CDOM with 273629 elements.
Creating vector time with 273629 elements.
Creating vector dissolvedO2 with 273629 elements.
Creating vector time with 273629 elements.
Creating vector salinity with 273629 elements.
Creating vector time with 273629 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/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/2022/2022138/2022.138.00/ctdDriver2.nc')
Creating vector time with 273500 elements.
Creating vector conductivity with 273500 elements.
Creating vector time with 273500 elements.
Creating vector temperature with 273500 elements.
Creating vector time with 273500 elements.
Creating vector cond_frequency with 273500 elements.
Creating vector time with 273500 elements.
Creating vector temp_frequency with 273500 elements.
Creating vector time with 273500 elements.
Creating vector flow2 with 273500 elements.
Creating vector time with 273500 elements.
Creating vector par with 273500 elements.
Creating vector time with 273500 elements.
Creating vector spare with 273500 elements.
Creating vector time with 273500 elements.
Creating vector salinity with 273500 elements.
Creating vector time with 273500 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/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/2022/2022138/2022.138.00/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/2022/2022138/2022.138.00/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/2022/2022138/2022.138.00/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/2022/2022138/2022.138.00/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/2022/2022138/2022.138.00/biolume.nc')
Creating vector time with 67274 elements.
Creating vector rrr with 67274 elements.
Creating vector time with 67274 elements.
Creating vector cal_striing with 67274 elements.
Creating vector time with 67274 elements.
Creating vector avg_biolume with 67274 elements.
Creating vector time with 67274 elements.
Creating vector pump with 67274 elements.
Creating vector time with 67274 elements.
Creating vector system_voltage with 67274 elements.
Creating vector time with 67274 elements.
Creating vector flow with 67274 elements.
Creating vector time with 67274 elements.
Creating vector HV with 67274 elements.
Creating vector time with 67274 elements.
Creating vector reserved with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_0 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_1 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_2 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_3 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_4 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_5 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_6 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_7 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_8 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_9 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_10 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_11 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_12 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_13 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_14 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_15 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_16 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_17 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_18 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_19 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_20 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_21 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_22 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_23 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_24 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_25 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_26 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_27 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_28 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_29 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_30 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_31 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_32 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_33 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_34 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_35 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_36 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_37 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_38 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_39 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_40 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_41 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_42 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_43 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_44 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_45 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_46 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_47 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_48 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_49 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_50 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_51 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_52 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_53 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_54 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_55 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_56 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_57 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_58 with 67274 elements.
Creating vector time with 67274 elements.
Creating vector raw_59 with 67274 elements.
Creating vector time with 67274 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/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/2022/2022138/2022.138.00/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (6516 x 994) with 6476904 elements.
Creating vector time with 6516 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (6516 x 994) with 6476904 elements.
Creating vector time with 6516 elements.
Creating vector bin with 994 elements.
Creating matrix countList (6516 x 994) with 6476904 elements.
Creating vector time with 6516 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 6516 elements.
Creating vector time with 6516 elements.
Creating vector transCount with 6516 elements.
Creating vector time with 6516 elements.
Creating vector nonTransCount with 6516 elements.
Creating vector time with 6516 elements.
Creating vector ai_mean with 6516 elements.
Creating vector time with 6516 elements.
Creating vector ai_min with 6516 elements.
Creating vector time with 6516 elements.
Creating vector ai_max with 6516 elements.
Creating vector time with 6516 elements.
Creating vector ai_std with 6516 elements.
Creating vector time with 6516 elements.
Creating vector esd_mean with 6516 elements.
Creating vector time with 6516 elements.
Creating vector esd_min with 6516 elements.
Creating vector time with 6516 elements.
Creating vector esd_max with 6516 elements.
Creating vector time with 6516 elements.
Creating vector esd_std with 6516 elements.
Creating vector time with 6516 elements.
Creating vector countSum with 6516 elements.
Creating vector time with 6516 elements.
Creating vector snapshot with 6516 elements.
Creating vector time with 6516 elements.
Creating vector threshold with 6516 elements.
Creating vector time with 6516 elements.
Creating vector sampleCount with 6516 elements.
Creating vector time with 6516 elements.
Creating vector flowCount with 6516 elements.
Creating vector time with 6516 elements.
Creating vector flowTime with 6516 elements.
Creating vector time with 6516 elements.
Creating vector bufferStatus with 6516 elements.
Creating vector time with 6516 elements.
Creating vector laserLevel with 6516 elements.
Creating vector time with 6516 elements.
Creating vector counter with 6516 elements.
Creating vector time with 6516 elements.
Creating vector counterPeriod with 6516 elements.
Creating vector time with 6516 elements.
Creating vector laserControl with 6516 elements.
Creating vector time with 6516 elements.
Creating vector countUnknownFrameCharacter with 6516 elements.
Creating vector time with 6516 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 6516 elements.
Creating vector time with 6516 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 6516 elements.
Creating vector time with 6516 elements.
Creating vector flowSpeed with 6516 elements.
Creating vector time with 6516 elements.
Creating vector countShortLFrameError with 6516 elements.
Creating vector time with 6516 elements.
Creating vector countGarbledLFrame with 6516 elements.
Creating vector time with 6516 elements.
Creating vector cFrameEsecs with 6516 elements.
Creating vector time with 6516 elements.
Creating vector correctedSampleCountList with 6516 elements.
Creating vector time with 6516 elements.
Creating vector time with 6516 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022138/2022.138.00/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022.138.00.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_2022.138.00.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_138_00_138_00_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_138_00_138_00.mat
Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_138_00_138_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 = 430 Gridding with nix = 1290, iZ = 403
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 336606 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 336606 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 154017 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 05/18/2022 11:30  to 05/19/2022 08:30 

swr =

  959.6746
       NaN
       NaN
  960.6901
  845.4534
  641.7541
  448.0916
  247.0586
   67.7403
    8.4781
    6.1219
    6.2333
    6.3184
    6.2816
    6.3401
    6.4782
    6.4552
    6.4264
    7.3237
   58.4545
  238.0603
  517.9840

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_138_00_138_00_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2022138_GulperTimes.txt && touch ../results/2022138_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/2022/2022138/2022.138.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2022/2022138/2022.138.00/syslog -startEsecs 1652904294.8138 -surveyName Dorado389_2022_138_00_138_00 >> ../results/2022138_GulperTimes.txt
Executing: removeGulpDups.py ../results/2022138_GulperTimes.txt
Bottle: 0 Time: 1652906910.2146 Depth: 149.9927 Dist: 2.2145
Bottle: 1 Time: 1652907043.2155 Depth: 99.9658 Dist: 2.3605
Bottle: 2 Time: 1652907152.408 Depth: 59.9984 Dist: 2.4782
Bottle: 3 Time: 1652907260.6106 Depth: 19.9313 Dist: 2.5891
Bottle: 4 Time: 1652907310.8072 Depth: 4.9259 Dist: 2.6427
Bottle: 5 Time: 1652910841.0154 Depth: 5.0046 Dist: 6.9399
Bottle: 6 Time: 1652913995.4093 Depth: 5.0781 Dist: 11.0163
Bottle: 7 Time: 1652917284.014 Depth: 5.0471 Dist: 15.0631
Bottle: 8 Time: 1652920547.8104 Depth: 3.6743 Dist: 19.0053
Bottle: 9 Time: 1652924208.8096 Depth: 5.0031 Dist: 23.3973
Bottle: 10 Time: 1652927874.8085 Depth: 5.0587 Dist: 27.6812
Bottle: 11 Time: 1652931324.6121 Depth: 5.0285 Dist: 31.6767
Bottle: 12 Time: 1652934908.0066 Depth: 5.0006 Dist: 36.0077
Bottle: 13 Time: 1652940220.8127 Depth: 5.0249 Dist: 42.0261
Bottle: 14 Time: 1652943795.2578 Depth: 5.1413 Dist: 46.4314
Bottle: 15 Time: 1652947434.0086 Depth: 5.0025 Dist: 50.9974
Bottle: 16 Time: 1652950858.614 Depth: 5.0402 Dist: 55.1717
Bottle: 17 Time: 1652954481.2158 Depth: -0.082326 Dist: 59.0678
Bottle: 18 Time: 1652957855.2747 Depth: 5.0241 Dist: 63.0829
Bottle: 19 Time: 1652961089.4131 Depth: 5.0592 Dist: 66.9532
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_138_00_138_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_2022_138_00_138_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_2022_138_00_138_00_biolume.png
Elapsed time to save image: 49 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_138_00_138_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_138_00_138_00_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_138_00_138_00_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_138_00_138_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_138_00_138_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_138_00_138_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_138_00_138_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_138_00_138_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_138_00_138_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) = 2022-05-18T20:04:54Z
gmtstr(tend) = 2022-05-19T15:04:48Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
3 NaNs found in bbpBlue.  Interpolating anyway.
3 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_138_00_138_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_00_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_00_Salinity.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_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.
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_00_Nitrate.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_00_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_00_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_00_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_00_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_00_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_00_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_138_00_138_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_138_00_138_00.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_138_00_138_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_138_00_138_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_138_00_138_00.mat ...
Iterpolating to 2 second increments between Nav time bounds...
gmtstr(tstart) = 2022-05-18T20:04:54Z
gmtstr(tend) = 2022-05-19T15:04:48Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
3 NaNs found in bbpBlue.  Interpolating anyway.
3 NaNs found in bbpRed.  Interpolating anyway.
Encountered 536 NaN values in array of lon that is 34197 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 33661 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 33661 are not equal to number of Lat lon points = 34197
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_138_00_138_00.txt
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_138_00_138_00_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_138_00_138_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_138_00_138_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_138_00_138_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_138_00_138_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_138_00_138_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_138_00_138_00.nc
 
 
*************************************************************************
Composing email to send to auvctd@listserver.mbari.org ...
!mail -s "Survey Dorado389_2022_138_00_138_00 processed" auvctd@listserver.mbari.org < mail_Dorado389_2022_138_00_138_00.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022.138.00.mat
Processing time: 839 seconds