Execution of AUVprocess_main version 1.88 at 2022-03-22T21:05:17Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2022, ['054.01'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1')
 
*************************************************************************
Processing data from SSDS via DODS server
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2022.054.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/
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/2022/2022054/2022.054.01/navigation.nc')
Creating vector time with 354073 elements.
Creating vector mPos_x with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mPos_y with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mDepth with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mGpsNorth with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mGpsEast with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mGpsValid with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mPhi with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mTheta with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mPsi with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mOmega_x with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mOmega_y with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mOmega_z with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mPsaRange with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mAltitude with 354073 elements.
Creating vector time with 354073 elements.
Creating vector multibeamAltitude with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mDvlAltitude with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mEchoAltitude with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mEchoHorizRange with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mEchoAltitudeLast with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mEchoHorizRangeLast with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mEchoNumOfPings with 354073 elements.
Creating vector time with 354073 elements.
Creating vector nadirCnts with 354073 elements.
Creating vector time with 354073 elements.
Creating vector obstacleCnts with 354073 elements.
Creating vector time with 354073 elements.
Creating vector nGoodNadirBeams with 354073 elements.
Creating vector time with 354073 elements.
Creating vector medianNadirBeamNo with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mWaterSpeed with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mDvlValid with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mDvlNewData with 354073 elements.
Creating vector time with 354073 elements.
Creating vector mDeltaT with 354073 elements.
Creating vector time with 354073 elements.
Creating vector nfix with 354073 elements.
Creating vector time with 354073 elements.
Creating vector efix with 354073 elements.
Creating vector time with 354073 elements.
Creating vector filter_north with 354073 elements.
Creating vector time with 354073 elements.
Creating vector filter_east with 354073 elements.
Creating vector time with 354073 elements.
Creating vector filter_depth with 354073 elements.
Creating vector time with 354073 elements.
Creating vector north_current with 354073 elements.
Creating vector time with 354073 elements.
Creating vector east_current with 354073 elements.
Creating vector time with 354073 elements.
Creating vector speed_bias with 354073 elements.
Creating vector time with 354073 elements.
Creating vector heading_bias with 354073 elements.
Creating vector time with 354073 elements.
Creating vector latitude with 354073 elements.
Creating vector time with 354073 elements.
Creating vector longitude with 354073 elements.
Creating vector time with 354073 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/navigation.nc');
processNav(): median of positive valued depths = 28.4311
processNav(): Finding depths less than 284.3108 and times > 0
processNav(): length(Nav.depth) = 354073
processNav(): length(gindx)     = 354073
 
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/2022/2022054/2022.054.01/gps.nc')
Creating vector time with 16627 elements.
Creating vector hours with 16627 elements.
Creating vector time with 16627 elements.
Creating vector minutes with 16627 elements.
Creating vector time with 16627 elements.
Creating vector seconds with 16627 elements.
Creating vector time with 16627 elements.
Creating vector centiSeconds with 16627 elements.
Creating vector time with 16627 elements.
Creating vector latitude with 16627 elements.
Creating vector time with 16627 elements.
Creating vector longitude with 16627 elements.
Creating vector time with 16627 elements.
Creating vector quality with 16627 elements.
Creating vector time with 16627 elements.
Creating vector numberOfSatellites with 16627 elements.
Creating vector time with 16627 elements.
Creating vector hdop with 16627 elements.
Creating vector time with 16627 elements.
Creating vector antennaHeight with 16627 elements.
Creating vector time with 16627 elements.
Creating vector geoHeight with 16627 elements.
Creating vector time with 16627 elements.
Creating vector dgpsDataAge with 16627 elements.
Creating vector time with 16627 elements.
Creating vector dgpsRSID with 16627 elements.
Creating vector time with 16627 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/gps.nc');
 
Processing depth data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/parosci.nc')
Creating vector time with 705130 elements.
Creating vector depth with 705130 elements.
Creating vector time with 705130 elements.
Creating vector temp with 705130 elements.
Creating vector time with 705130 elements.
Creating vector pressure with 705130 elements.
Creating vector time with 705130 elements.
Creating vector temp_period with 705130 elements.
Creating vector time with 705130 elements.
Creating vector pres_period with 705130 elements.
Creating vector time with 705130 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.19567 max(Depth.data) = 203.0148
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.19567 max(Depth.data) = 203.0148
 
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/2022/2022054/2022.054.01/hydroscatlog.nc')
Creating vector time with 283270 elements.
Creating vector Seconds with 283270 elements.
Creating vector time with 283270 elements.
Creating vector HundrethsOfSeconds with 283270 elements.
Creating vector time with 283270 elements.
Creating vector Snorm1 with 283270 elements.
Creating vector time with 283270 elements.
Creating vector Snorm2 with 283270 elements.
Creating vector time with 283270 elements.
Creating vector Snorm3 with 283270 elements.
Creating vector time with 283270 elements.
Creating vector Gain_Status_1 with 283270 elements.
Creating vector time with 283270 elements.
Creating vector Gain_Status_2 with 283270 elements.
Creating vector time with 283270 elements.
Creating vector Gain_Status_3 with 283270 elements.
Creating vector time with 283270 elements.
Creating vector RawDepthValue with 283270 elements.
Creating vector time with 283270 elements.
Creating vector RawTempValue with 283270 elements.
Creating vector time with 283270 elements.
Creating vector Temperature with 283270 elements.
Creating vector time with 283270 elements.
Creating vector ErrorValue with 283270 elements.
Creating vector time with 283270 elements.
Creating vector bb470 with 283270 elements.
Creating vector time with 283270 elements.
Creating vector bb676 with 283270 elements.
Creating vector time with 283270 elements.
Creating vector fl676u with 283270 elements.
Creating vector time with 283270 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/hydroscatlog.nc');
 
Processing CTD #1 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/ctdDriver.nc')
Creating vector time with 283314 elements.
Creating vector conductivity with 283314 elements.
Creating vector time with 283314 elements.
Creating vector temperature with 283314 elements.
Creating vector time with 283314 elements.
Creating vector cond_frequency with 283314 elements.
Creating vector time with 283314 elements.
Creating vector temp_frequency with 283314 elements.
Creating vector time with 283314 elements.
Creating vector spare with 283314 elements.
Creating vector time with 283314 elements.
Creating vector humidity with 283314 elements.
Creating vector time with 283314 elements.
Creating vector flow1 with 283314 elements.
Creating vector time with 283314 elements.
Creating vector CDOM with 283314 elements.
Creating vector time with 283314 elements.
Creating vector dissolvedO2 with 283314 elements.
Creating vector time with 283314 elements.
Creating vector salinity with 283314 elements.
Creating vector time with 283314 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/ctdDriver.cfg
Oxygen calibration loaded from CTD config file (current method)
Using constant flow rate offset for oxygen...
 
Processing CTD #2 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/ctdDriver2.nc')
Creating vector time with 283274 elements.
Creating vector conductivity with 283274 elements.
Creating vector time with 283274 elements.
Creating vector temperature with 283274 elements.
Creating vector time with 283274 elements.
Creating vector cond_frequency with 283274 elements.
Creating vector time with 283274 elements.
Creating vector temp_frequency with 283274 elements.
Creating vector time with 283274 elements.
Creating vector flow2 with 283274 elements.
Creating vector time with 283274 elements.
Creating vector par with 283274 elements.
Creating vector time with 283274 elements.
Creating vector spare with 283274 elements.
Creating vector time with 283274 elements.
Creating vector salinity with 283274 elements.
Creating vector time with 283274 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/ctdDriver2.cfg
 
Processing ISUS data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/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/2022/2022054/2022.054.01/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/2022/2022054/2022.054.01/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/2022/2022054/2022.054.01/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/2022/2022054/2022.054.01/biolume.nc')
Creating vector time with 69651 elements.
Creating vector rrr with 69651 elements.
Creating vector time with 69651 elements.
Creating vector cal_striing with 69651 elements.
Creating vector time with 69651 elements.
Creating vector avg_biolume with 69651 elements.
Creating vector time with 69651 elements.
Creating vector pump with 69651 elements.
Creating vector time with 69651 elements.
Creating vector system_voltage with 69651 elements.
Creating vector time with 69651 elements.
Creating vector flow with 69651 elements.
Creating vector time with 69651 elements.
Creating vector HV with 69651 elements.
Creating vector time with 69651 elements.
Creating vector reserved with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_0 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_1 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_2 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_3 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_4 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_5 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_6 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_7 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_8 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_9 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_10 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_11 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_12 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_13 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_14 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_15 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_16 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_17 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_18 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_19 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_20 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_21 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_22 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_23 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_24 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_25 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_26 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_27 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_28 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_29 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_30 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_31 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_32 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_33 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_34 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_35 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_36 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_37 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_38 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_39 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_40 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_41 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_42 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_43 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_44 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_45 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_46 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_47 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_48 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_49 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_50 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_51 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_52 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_53 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_54 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_55 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_56 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_57 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_58 with 69651 elements.
Creating vector time with 69651 elements.
Creating vector raw_59 with 69651 elements.
Creating vector time with 69651 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (6747 x 994) with 6706518 elements.
Creating vector time with 6747 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (6747 x 994) with 6706518 elements.
Creating vector time with 6747 elements.
Creating vector bin with 994 elements.
Creating matrix countList (6747 x 994) with 6706518 elements.
Creating vector time with 6747 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 6747 elements.
Creating vector time with 6747 elements.
Creating vector transCount with 6747 elements.
Creating vector time with 6747 elements.
Creating vector nonTransCount with 6747 elements.
Creating vector time with 6747 elements.
Creating vector ai_mean with 6747 elements.
Creating vector time with 6747 elements.
Creating vector ai_min with 6747 elements.
Creating vector time with 6747 elements.
Creating vector ai_max with 6747 elements.
Creating vector time with 6747 elements.
Creating vector ai_std with 6747 elements.
Creating vector time with 6747 elements.
Creating vector esd_mean with 6747 elements.
Creating vector time with 6747 elements.
Creating vector esd_min with 6747 elements.
Creating vector time with 6747 elements.
Creating vector esd_max with 6747 elements.
Creating vector time with 6747 elements.
Creating vector esd_std with 6747 elements.
Creating vector time with 6747 elements.
Creating vector countSum with 6747 elements.
Creating vector time with 6747 elements.
Creating vector snapshot with 6747 elements.
Creating vector time with 6747 elements.
Creating vector threshold with 6747 elements.
Creating vector time with 6747 elements.
Creating vector sampleCount with 6747 elements.
Creating vector time with 6747 elements.
Creating vector flowCount with 6747 elements.
Creating vector time with 6747 elements.
Creating vector flowTime with 6747 elements.
Creating vector time with 6747 elements.
Creating vector bufferStatus with 6747 elements.
Creating vector time with 6747 elements.
Creating vector laserLevel with 6747 elements.
Creating vector time with 6747 elements.
Creating vector counter with 6747 elements.
Creating vector time with 6747 elements.
Creating vector counterPeriod with 6747 elements.
Creating vector time with 6747 elements.
Creating vector laserControl with 6747 elements.
Creating vector time with 6747 elements.
Creating vector countUnknownFrameCharacter with 6747 elements.
Creating vector time with 6747 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 6747 elements.
Creating vector time with 6747 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 6747 elements.
Creating vector time with 6747 elements.
Creating vector flowSpeed with 6747 elements.
Creating vector time with 6747 elements.
Creating vector countShortLFrameError with 6747 elements.
Creating vector time with 6747 elements.
Creating vector countGarbledLFrame with 6747 elements.
Creating vector time with 6747 elements.
Creating vector cFrameEsecs with 6747 elements.
Creating vector time with 6747 elements.
Creating vector correctedSampleCountList with 6747 elements.
Creating vector time with 6747 elements.
Creating vector time with 6747 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2022/2022054/2022.054.01/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022.054.01.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_2022.054.01.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_054_01_054_01_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_054_01_054_01.mat
Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_054_01_054_01.mat
 
 
*************************************************************************
Calling plot_sections from ../viz to produce section plots ...
Using median boxcar filter of vector...
Using mean boxcar filter of vector...
Number of profiles found = 442 Gridding with nix = 1326, 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 338479 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 338479 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 = 26351.8726 since 1/1/1950
Looking for end   days = 26352.6922
sIndx = 
eIndx = 
Met data goes from 20017.6042 to 26097.7292
No SWR data loaded from URL.
Executing: /bin/rm -f ../results/2022054_GulperTimes.txt && touch ../results/2022054_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/2022/2022054/2022.054.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2022/2022054/2022.054.01/syslog -startEsecs 1645649794.3399 -surveyName Dorado389_2022_054_01_054_01 >> ../results/2022054_GulperTimes.txt
Executing: removeGulpDups.py ../results/2022054_GulperTimes.txt
Bottle: 0 Time: 1645653368.535 Depth: 149.8143 Dist: 3.4387
Bottle: 1 Time: 1645653526.7342 Depth: 99.8255 Dist: 3.6092
Bottle: 2 Time: 1645653657.3353 Depth: 59.8041 Dist: 3.7455
Bottle: 3 Time: 1645653789.5362 Depth: 19.7789 Dist: 3.8807
Bottle: 4 Time: 1645653852.5419 Depth: 4.7875 Dist: 3.9438
Bottle: 5 Time: 1645657216.7414 Depth: 5.2324 Dist: 8.2085
Bottle: 6 Time: 1645660057.7368 Depth: 5.1955 Dist: 12.196
Bottle: 7 Time: 1645663116.3373 Depth: 5.1761 Dist: 16.236
Bottle: 8 Time: 1645666334.7368 Depth: 5.2679 Dist: 20.1524
Bottle: 9 Time: 1645669941.5397 Depth: 5.2077 Dist: 24.4956
Bottle: 10 Time: 1645673181.1378 Depth: 5.1665 Dist: 28.4401
Bottle: 11 Time: 1645676739.134 Depth: 5.3011 Dist: 32.7937
Bottle: 12 Time: 1645680116.7327 Depth: 5.2656 Dist: 36.7879
Bottle: 13 Time: 1645684953.9413 Depth: 5.2143 Dist: 42.2412
Bottle: 14 Time: 1645688460.3411 Depth: 5.1812 Dist: 46.6459
Bottle: 15 Time: 1645691887.5363 Depth: 5.2653 Dist: 50.9639
Bottle: 16 Time: 1645695444.9326 Depth: 4.2205 Dist: 55.2929
Bottle: 17 Time: 1645698709.939 Depth: 5.3462 Dist: 59.1857
Bottle: 18 Time: 1645702177.3414 Depth: 5.2555 Dist: 63.244
Bottle: 19 Time: 1645705566.7392 Depth: 5.2957 Dist: 67.2321
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_054_01_054_01_gridded.mat

outvarstr =

    'gF gT gN gS gD gO gB420 gB700 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth '

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_054_01_054_01_2column.png
Elapsed time to save image: 12 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_054_01_054_01_biolume.png
Elapsed time to save image: 73 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_054_01_054_01_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_054_01_054_01_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_054_01_054_01_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_054_01_054_01_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_054_01_054_01_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_054_01_054_01_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_054_01_054_01_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_054_01_054_01_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_054_01_054_01_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) = 2022-02-23T20:56:34Z
gmtstr(tend) = 2022-02-24T16:36:48Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
10 NaNs found in bbpBlue.  Interpolating anyway.
34 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_054_01_054_01_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_054_01_054_01_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_054_01_054_01_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_054_01_054_01_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_054_01_054_01_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_054_01_054_01_Nitrate.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_054_01_054_01_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_054_01_054_01_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_054_01_054_01_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_054_01_054_01_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_054_01_054_01_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_054_01_054_01_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_054_01_054_01_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_054_01_054_01_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_054_01_054_01_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_054_01_054_01_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_054_01_054_01_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_054_01_054_01_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2022_054_01_054_01_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_054_01_054_01.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_054_01_054_01.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_054_01_054_01_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_054_01_054_01.mat ...
Iterpolating to 2 second increments between Nav time bounds...
gmtstr(tstart) = 2022-02-23T20:56:34Z
gmtstr(tend) = 2022-02-24T16:36:48Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
10 NaNs found in bbpBlue.  Interpolating anyway.
34 NaNs found in bbpRed.  Interpolating anyway.
Encountered 1561 NaN values in array of lon that is 35408 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 33847 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 33847 are not equal to number of Lat lon points = 35408
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_054_01_054_01.txt
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_054_01_054_01_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022_054_01_054_01.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_054_01_054_01_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_054_01_054_01.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_054_01_054_01_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_054_01_054_01.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_054_01_054_01.nc
 
 
*************************************************************************
Composing email to send to auvctd@listserver.mbari.org ...
!mail -s "Survey Dorado389_2022_054_01_054_01 processed" auvctd@listserver.mbari.org < mail_Dorado389_2022_054_01_054_01.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2022.054.01.mat
Processing time: 618 seconds