Execution of AUVprocess_main version 1.86 at 2017-10-03T03:58:58Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2017, ['269.01'], '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: 2017.269.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/
Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Processing DVL navigation data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/navigation.nc')
Creating vector time with 395591 elements.
Creating vector mPos_x with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mPos_y with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mDepth with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mGpsNorth with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mGpsEast with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mGpsValid with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mPhi with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mTheta with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mPsi with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mOmega_x with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mOmega_y with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mOmega_z with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mPsaRange with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mAltitude with 395591 elements.
Creating vector time with 395591 elements.
Creating vector multibeamAltitude with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mDvlAltitude with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mEchoAltitude with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mEchoHorizRange with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mEchoAltitudeLast with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mEchoHorizRangeLast with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mEchoNumOfPings with 395591 elements.
Creating vector time with 395591 elements.
Creating vector nadirCnts with 395591 elements.
Creating vector time with 395591 elements.
Creating vector obstacleCnts with 395591 elements.
Creating vector time with 395591 elements.
Creating vector nGoodNadirBeams with 395591 elements.
Creating vector time with 395591 elements.
Creating vector medianNadirBeamNo with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mWaterSpeed with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mDvlValid with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mDvlNewData with 395591 elements.
Creating vector time with 395591 elements.
Creating vector mDeltaT with 395591 elements.
Creating vector time with 395591 elements.
Creating vector nfix with 395591 elements.
Creating vector time with 395591 elements.
Creating vector efix with 395591 elements.
Creating vector time with 395591 elements.
Creating vector filter_north with 395591 elements.
Creating vector time with 395591 elements.
Creating vector filter_east with 395591 elements.
Creating vector time with 395591 elements.
Creating vector filter_depth with 395591 elements.
Creating vector time with 395591 elements.
Creating vector north_current with 395591 elements.
Creating vector time with 395591 elements.
Creating vector east_current with 395591 elements.
Creating vector time with 395591 elements.
Creating vector speed_bias with 395591 elements.
Creating vector time with 395591 elements.
Creating vector heading_bias with 395591 elements.
Creating vector time with 395591 elements.
Creating vector latitude with 395591 elements.
Creating vector time with 395591 elements.
Creating vector longitude with 395591 elements.
Creating vector time with 395591 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/navigation.nc');
processNav(): median of positive valued depths = 40.7687
processNav(): Finding depths less than 203.8437 and times > 0
processNav(): length(Nav.depth) = 395591
processNav(): length(gindx)     = 395591
 
Processing GPS navigation data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/gps.nc')
Creating vector time with 4794 elements.
Creating vector hours with 4794 elements.
Creating vector time with 4794 elements.
Creating vector minutes with 4794 elements.
Creating vector time with 4794 elements.
Creating vector seconds with 4794 elements.
Creating vector time with 4794 elements.
Creating vector centiSeconds with 4794 elements.
Creating vector time with 4794 elements.
Creating vector latitude with 4794 elements.
Creating vector time with 4794 elements.
Creating vector longitude with 4794 elements.
Creating vector time with 4794 elements.
Creating vector quality with 4794 elements.
Creating vector time with 4794 elements.
Creating vector numberOfSatellites with 4794 elements.
Creating vector time with 4794 elements.
Creating vector hdop with 4794 elements.
Creating vector time with 4794 elements.
Creating vector antennaHeight with 4794 elements.
Creating vector time with 4794 elements.
Creating vector geoHeight with 4794 elements.
Creating vector time with 4794 elements.
Creating vector dgpsDataAge with 4794 elements.
Creating vector time with 4794 elements.
Creating vector dgpsRSID with 4794 elements.
Creating vector time with 4794 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/gps.nc');
processGPS(): *** skipping bad position (lat,lon) = 74.896, -124.9984
processGPS(): *** skipping bad position (lat,lon) = 74.914, -125.0159
processGPS(): *** skipping bad position (lat,lon) = 74.932, -125.0334
processGPS(): *** skipping bad position (lat,lon) = 74.9499, -125.051
processGPS(): *** skipping bad position (lat,lon) = 74.9679, -125.0686
processGPS(): *** skipping bad position (lat,lon) = 74.9858, -125.0863
processGPS(): *** skipping bad position (lat,lon) = 75.0038, -125.104
processGPS(): *** skipping bad position (lat,lon) = 75.0217, -125.1218
processGPS(): *** skipping bad position (lat,lon) = 75.0396, -125.1397
processGPS(): *** skipping bad position (lat,lon) = 75.0754, -125.1756
processGPS(): *** skipping bad position (lat,lon) = 75.0934, -125.1936
processGPS(): *** skipping bad position (lat,lon) = 75.3079, -125.4148
processGPS(): *** skipping bad position (lat,lon) = 77.8292, -128.9074
processGPS(): *** skipping bad position (lat,lon) = 77.8966, -129.0296
 
Processing depth data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/parosci.nc')
Creating vector time with 776243 elements.
Creating vector depth with 776243 elements.
Creating vector time with 776243 elements.
Creating vector temp with 776243 elements.
Creating vector time with 776243 elements.
Creating vector pressure with 776243 elements.
Creating vector time with 776243 elements.
Creating vector temp_period with 776243 elements.
Creating vector time with 776243 elements.
Creating vector pres_period with 776243 elements.
Creating vector time with 776243 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.29469 max(Depth.data) = 101.6472
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.29469 max(Depth.data) = 101.6472
 
Processing hs2 backscattering and chlorophyll fluorescence data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/hydroscatlog.nc')
Creating vector time with 313239 elements.
Creating vector Seconds with 313239 elements.
Creating vector time with 313239 elements.
Creating vector HundrethsOfSeconds with 313239 elements.
Creating vector time with 313239 elements.
Creating vector Snorm1 with 313239 elements.
Creating vector time with 313239 elements.
Creating vector Snorm2 with 313239 elements.
Creating vector time with 313239 elements.
Creating vector Snorm3 with 313239 elements.
Creating vector time with 313239 elements.
Creating vector Gain_Status_1 with 313239 elements.
Creating vector time with 313239 elements.
Creating vector Gain_Status_2 with 313239 elements.
Creating vector time with 313239 elements.
Creating vector Gain_Status_3 with 313239 elements.
Creating vector time with 313239 elements.
Creating vector RawDepthValue with 313239 elements.
Creating vector time with 313239 elements.
Creating vector RawTempValue with 313239 elements.
Creating vector time with 313239 elements.
Creating vector Temperature with 313239 elements.
Creating vector time with 313239 elements.
Creating vector ErrorValue with 313239 elements.
Creating vector time with 313239 elements.
Creating vector bb470 with 313239 elements.
Creating vector time with 313239 elements.
Creating vector bb676 with 313239 elements.
Creating vector time with 313239 elements.
Creating vector fl676u with 313239 elements.
Creating vector time with 313239 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/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/2017/2017269/2017.269.01/ctdDriver.nc')
Creating vector time with 313643 elements.
Creating vector conductivity with 313643 elements.
Creating vector time with 313643 elements.
Creating vector temperature with 313643 elements.
Creating vector time with 313643 elements.
Creating vector cond_frequency with 313643 elements.
Creating vector time with 313643 elements.
Creating vector temp_frequency with 313643 elements.
Creating vector time with 313643 elements.
Creating vector spare with 313643 elements.
Creating vector time with 313643 elements.
Creating vector humidity with 313643 elements.
Creating vector time with 313643 elements.
Creating vector flow1 with 313643 elements.
Creating vector time with 313643 elements.
Creating vector CDOM with 313643 elements.
Creating vector time with 313643 elements.
Creating vector dissolvedO2 with 313643 elements.
Creating vector time with 313643 elements.
Creating vector salinity with 313643 elements.
Creating vector time with 313643 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/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/2017/2017269/2017.269.01/ctdDriver2.nc')
Creating vector time with 313396 elements.
Creating vector conductivity with 313396 elements.
Creating vector time with 313396 elements.
Creating vector temperature with 313396 elements.
Creating vector time with 313396 elements.
Creating vector cond_frequency with 313396 elements.
Creating vector time with 313396 elements.
Creating vector temp_frequency with 313396 elements.
Creating vector time with 313396 elements.
Creating vector flow2 with 313396 elements.
Creating vector time with 313396 elements.
Creating vector spare with 313396 elements.
Creating vector time with 313396 elements.
Creating vector salinity with 313396 elements.
Creating vector time with 313396 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/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/2017/2017269/2017.269.01/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/2017/2017269/2017.269.01/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/2017/2017269/2017.269.01/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/2017/2017269/2017.269.01/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 66)
  In processBiolume (line 21)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
[Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 66)
  In processBiolume (line 22)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/biolume.nc')
Creating vector time with 77747 elements.
Creating vector rrr with 77747 elements.
Creating vector time with 77747 elements.
Creating vector cal_striing with 77747 elements.
Creating vector time with 77747 elements.
Creating vector avg_biolume with 77747 elements.
Creating vector time with 77747 elements.
Creating vector pump with 77747 elements.
Creating vector time with 77747 elements.
Creating vector system_voltage with 77747 elements.
Creating vector time with 77747 elements.
Creating vector flow with 77747 elements.
Creating vector time with 77747 elements.
Creating vector HV with 77747 elements.
Creating vector time with 77747 elements.
Creating vector reserved with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_0 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_1 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_2 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_3 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_4 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_5 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_6 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_7 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_8 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_9 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_10 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_11 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_12 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_13 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_14 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_15 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_16 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_17 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_18 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_19 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_20 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_21 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_22 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_23 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_24 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_25 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_26 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_27 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_28 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_29 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_30 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_31 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_32 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_33 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_34 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_35 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_36 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_37 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_38 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_39 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_40 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_41 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_42 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_43 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_44 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_45 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_46 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_47 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_48 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_49 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_50 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_51 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_52 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_53 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_54 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_55 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_56 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_57 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_58 with 77747 elements.
Creating vector time with 77747 elements.
Creating vector raw_59 with 77747 elements.
Creating vector time with 77747 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/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/2017/2017269/2017.269.01/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (7509 x 994) with 7463946 elements.
Creating vector time with 7509 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (7509 x 994) with 7463946 elements.
Creating vector time with 7509 elements.
Creating vector bin with 994 elements.
Creating matrix countList (7509 x 994) with 7463946 elements.
Creating vector time with 7509 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 7509 elements.
Creating vector time with 7509 elements.
Creating vector transCount with 7509 elements.
Creating vector time with 7509 elements.
Creating vector nonTransCount with 7509 elements.
Creating vector time with 7509 elements.
Creating vector ai_mean with 7509 elements.
Creating vector time with 7509 elements.
Creating vector ai_min with 7509 elements.
Creating vector time with 7509 elements.
Creating vector ai_max with 7509 elements.
Creating vector time with 7509 elements.
Creating vector ai_std with 7509 elements.
Creating vector time with 7509 elements.
Creating vector esd_mean with 7509 elements.
Creating vector time with 7509 elements.
Creating vector esd_min with 7509 elements.
Creating vector time with 7509 elements.
Creating vector esd_max with 7509 elements.
Creating vector time with 7509 elements.
Creating vector esd_std with 7509 elements.
Creating vector time with 7509 elements.
Creating vector countSum with 7509 elements.
Creating vector time with 7509 elements.
Creating vector snapshot with 7509 elements.
Creating vector time with 7509 elements.
Creating vector threshold with 7509 elements.
Creating vector time with 7509 elements.
Creating vector sampleCount with 7509 elements.
Creating vector time with 7509 elements.
Creating vector flowCount with 7509 elements.
Creating vector time with 7509 elements.
Creating vector flowTime with 7509 elements.
Creating vector time with 7509 elements.
Creating vector bufferStatus with 7509 elements.
Creating vector time with 7509 elements.
Creating vector laserLevel with 7509 elements.
Creating vector time with 7509 elements.
Creating vector counter with 7509 elements.
Creating vector time with 7509 elements.
Creating vector counterPeriod with 7509 elements.
Creating vector time with 7509 elements.
Creating vector laserControl with 7509 elements.
Creating vector time with 7509 elements.
Creating vector countUnknownFrameCharacter with 7509 elements.
Creating vector time with 7509 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7509 elements.
Creating vector time with 7509 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7509 elements.
Creating vector time with 7509 elements.
Creating vector flowSpeed with 7509 elements.
Creating vector time with 7509 elements.
Creating vector countShortLFrameError with 7509 elements.
Creating vector time with 7509 elements.
Creating vector countGarbledLFrame with 7509 elements.
Creating vector time with 7509 elements.
Creating vector cFrameEsecs with 7509 elements.
Creating vector time with 7509 elements.
Creating vector correctedSampleCountList with 7509 elements.
Creating vector time with 7509 elements.
Creating vector time with 7509 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.269.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Calling build_auv_survey.m to construct survey file...

SecondaryDissolvedO2 =

     []

Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.269.01.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 30 segments.
[Warning: MATLAB has disabled some advanced graphics rendering features by
switching to software OpenGL. For more information, click <a
href="matlab:opengl('problems')">here</a>.] 
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_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 = 404 Gridding with nix = 1212, iZ = 200
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 394461 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 394461 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 113289 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 09/26/2017 08:30  to 09/27/2017 08:30 

swr =

  218.9073
  409.1377
  609.4838
  779.3227
  853.4766
  823.0546
  530.0772
  594.1572
  399.6647
  189.3644
   45.9198
    0.6774
    0.6635
    0.8247
    0.9548
    1.1795
    1.2247
    1.1814
    0.7646
    0.6400
    0.2753
    0.9896
    2.0016
   43.1289
  207.3705

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2017269_GulperTimes.txt && touch ../results/2017269_GulperTimes.txt
Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017269/2017.269.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2017/2017269/2017.269.01/syslog -startEsecs 1506448256.966 -surveyName Dorado389_2017_269_01_269_01 >> ../results/2017269_GulperTimes.txt
Executing: removeGulpDups.py ../results/2017269_GulperTimes.txt
Bottle: 0 Time: 1506460578.04 Depth: 8.6293 Dist: 14.8325
Bottle: 1 Time: 1506460618.64 Depth: 29.4845 Dist: 14.8838
Bottle: 2 Time: 1506469263.25 Depth: 4.7594 Dist: 25.1665
Bottle: 3 Time: 1506469332.04 Depth: 29.5159 Dist: 25.2532
Bottle: 4 Time: 1506476655.84 Depth: 3.2377 Dist: 34.5338
Bottle: 5 Time: 1506476714.45 Depth: 29.638 Dist: 34.612
Bottle: 6 Time: 1506486755.64 Depth: 9.3599 Dist: 46.3222
Bottle: 8 Time: 1506486755.66 Depth: 9.2615 Dist: 46.3225
Bottle: 7 Time: 1506486833.04 Depth: 29.4832 Dist: 46.4168
Bottle: 9 Time: 1506492883.24 Depth: 29.4757 Dist: 53.514
Bottle: 10 Time: 1506494081.65 Depth: 5.3897 Dist: 55.0492
Bottle: 11 Time: 1506494153.64 Depth: 29.4845 Dist: 55.1389
Bottle: 12 Time: 1506504224.64 Depth: 7.0979 Dist: 66.6092
Bottle: 14 Time: 1506504224.67 Depth: 6.9734 Dist: 66.6095
Bottle: 13 Time: 1506504295.85 Depth: 29.5661 Dist: 66.7043
Bottle: 15 Time: 1506510041.24 Depth: 29.4824 Dist: 74.2084
Bottle: 16 Time: 1506511655.64 Depth: 3.87 Dist: 76.3114
Bottle: 17 Time: 1506511722.25 Depth: 29.627 Dist: 76.3948
Bottle: 18 Time: 1506521967.25 Depth: 3.3358 Dist: 87.9691
Bottle: 19 Time: 1506522021.64 Depth: 29.524 Dist: 88.0374
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_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
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_2column.png
Elapsed time to save image: 33 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/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_biolume.png
Elapsed time to save image: 123 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/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_lopc.png
Elapsed time to save image: 32 seconds
 
 
*************************************************************************
Calling plot_survey_stats to produce histogram and profile statistics plots...
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_2column.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_biolume.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_lopc.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2017/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Nitrate.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_269_01_269_01_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2017_269_01_269_01.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01.kml...
Copied to /mbari/AUVCTD/surveys/2017/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_LOPC_Total_Count.kml'
not found.] 
[> In create_data_products (line 414)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01.mat ...
Iterpolating to 2 second increments between Nav time bounds...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
3 NaNs found in bbpBlue.  Interpolating anyway.
100 NaNs found in bbpRed.  Interpolating anyway.
152 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 0 NaN values in array of lon that is 31365 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 31365 points from grid Monterey25.grd (2876 x 2447)
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01.txt
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01.txt...
Copied to /mbari/AUVCTD/surveys/2017/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2017/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to 2 second increments between Nav time bounds...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
3 NaNs found in bbpBlue.  Interpolating anyway.
100 NaNs found in bbpRed.  Interpolating anyway.
152 NaNs found in flRed_uncorr.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_decim.nc...
Copied to /mbari/AUVCTD/surveys/2017/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing netCDF file ...
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01.nc...
Copied to /mbari/AUVCTD/surveys/2017/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2017/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_269_01_269_01.mat...
Copied to /mbari/AUVCTD/surveys/2017/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2017_269_01_269_01 processed" mccann@mbari.org < mail_Dorado389_2017_269_01_269_01.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.269.01.mat
Processing time: 691 seconds