Execution of AUVprocess_main version 1.87 at 2019-10-10T21:14:21Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2019, ['276.02'], '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: 2019.276.02
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/
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/2019/2019276/2019.276.02/navigation.nc')
Creating vector time with 492846 elements.
Creating vector mPos_x with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mPos_y with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mDepth with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mGpsNorth with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mGpsEast with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mGpsValid with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mPhi with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mTheta with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mPsi with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mOmega_x with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mOmega_y with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mOmega_z with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mPsaRange with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mAltitude with 492846 elements.
Creating vector time with 492846 elements.
Creating vector multibeamAltitude with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mDvlAltitude with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mEchoAltitude with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mEchoHorizRange with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mEchoAltitudeLast with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mEchoHorizRangeLast with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mEchoNumOfPings with 492846 elements.
Creating vector time with 492846 elements.
Creating vector nadirCnts with 492846 elements.
Creating vector time with 492846 elements.
Creating vector obstacleCnts with 492846 elements.
Creating vector time with 492846 elements.
Creating vector nGoodNadirBeams with 492846 elements.
Creating vector time with 492846 elements.
Creating vector medianNadirBeamNo with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mWaterSpeed with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mDvlValid with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mDvlNewData with 492846 elements.
Creating vector time with 492846 elements.
Creating vector mDeltaT with 492846 elements.
Creating vector time with 492846 elements.
Creating vector nfix with 492846 elements.
Creating vector time with 492846 elements.
Creating vector efix with 492846 elements.
Creating vector time with 492846 elements.
Creating vector filter_north with 492846 elements.
Creating vector time with 492846 elements.
Creating vector filter_east with 492846 elements.
Creating vector time with 492846 elements.
Creating vector filter_depth with 492846 elements.
Creating vector time with 492846 elements.
Creating vector north_current with 492846 elements.
Creating vector time with 492846 elements.
Creating vector east_current with 492846 elements.
Creating vector time with 492846 elements.
Creating vector speed_bias with 492846 elements.
Creating vector time with 492846 elements.
Creating vector heading_bias with 492846 elements.
Creating vector time with 492846 elements.
Creating vector latitude with 492846 elements.
Creating vector time with 492846 elements.
Creating vector longitude with 492846 elements.
Creating vector time with 492846 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/navigation.nc');
processNav(): median of positive valued depths = 100.9827
processNav(): Finding depths less than 706.8788 and times > 0
processNav(): length(Nav.depth) = 492846
processNav(): length(gindx)     = 492846
 
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/2019/2019276/2019.276.02/gps.nc')
Creating vector time with 9008 elements.
Creating vector hours with 9008 elements.
Creating vector time with 9008 elements.
Creating vector minutes with 9008 elements.
Creating vector time with 9008 elements.
Creating vector seconds with 9008 elements.
Creating vector time with 9008 elements.
Creating vector centiSeconds with 9008 elements.
Creating vector time with 9008 elements.
Creating vector latitude with 9008 elements.
Creating vector time with 9008 elements.
Creating vector longitude with 9008 elements.
Creating vector time with 9008 elements.
Creating vector quality with 9008 elements.
Creating vector time with 9008 elements.
Creating vector numberOfSatellites with 9008 elements.
Creating vector time with 9008 elements.
Creating vector hdop with 9008 elements.
Creating vector time with 9008 elements.
Creating vector antennaHeight with 9008 elements.
Creating vector time with 9008 elements.
Creating vector geoHeight with 9008 elements.
Creating vector time with 9008 elements.
Creating vector dgpsDataAge with 9008 elements.
Creating vector time with 9008 elements.
Creating vector dgpsRSID with 9008 elements.
Creating vector time with 9008 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/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/2019/2019276/2019.276.02/parosci.nc')
Creating vector time with 981351 elements.
Creating vector depth with 981351 elements.
Creating vector time with 981351 elements.
Creating vector temp with 981351 elements.
Creating vector time with 981351 elements.
Creating vector pressure with 981351 elements.
Creating vector time with 981351 elements.
Creating vector temp_period with 981351 elements.
Creating vector time with 981351 elements.
Creating vector pres_period with 981351 elements.
Creating vector time with 981351 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.47854 max(Depth.data) = 202.8003
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.47854 max(Depth.data) = 202.8003
 
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/2019/2019276/2019.276.02/hydroscatlog.nc')
Creating vector time with 394197 elements.
Creating vector Seconds with 394197 elements.
Creating vector time with 394197 elements.
Creating vector HundrethsOfSeconds with 394197 elements.
Creating vector time with 394197 elements.
Creating vector Snorm1 with 394197 elements.
Creating vector time with 394197 elements.
Creating vector Snorm2 with 394197 elements.
Creating vector time with 394197 elements.
Creating vector Snorm3 with 394197 elements.
Creating vector time with 394197 elements.
Creating vector Gain_Status_1 with 394197 elements.
Creating vector time with 394197 elements.
Creating vector Gain_Status_2 with 394197 elements.
Creating vector time with 394197 elements.
Creating vector Gain_Status_3 with 394197 elements.
Creating vector time with 394197 elements.
Creating vector RawDepthValue with 394197 elements.
Creating vector time with 394197 elements.
Creating vector RawTempValue with 394197 elements.
Creating vector time with 394197 elements.
Creating vector Temperature with 394197 elements.
Creating vector time with 394197 elements.
Creating vector ErrorValue with 394197 elements.
Creating vector time with 394197 elements.
Creating vector bb470 with 394197 elements.
Creating vector time with 394197 elements.
Creating vector bb676 with 394197 elements.
Creating vector time with 394197 elements.
Creating vector fl676u with 394197 elements.
Creating vector time with 394197 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/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/2019/2019276/2019.276.02/ctdDriver.nc')
Creating vector time with 394271 elements.
Creating vector conductivity with 394271 elements.
Creating vector time with 394271 elements.
Creating vector temperature with 394271 elements.
Creating vector time with 394271 elements.
Creating vector cond_frequency with 394271 elements.
Creating vector time with 394271 elements.
Creating vector temp_frequency with 394271 elements.
Creating vector time with 394271 elements.
Creating vector spare with 394271 elements.
Creating vector time with 394271 elements.
Creating vector humidity with 394271 elements.
Creating vector time with 394271 elements.
Creating vector flow1 with 394271 elements.
Creating vector time with 394271 elements.
Creating vector CDOM with 394271 elements.
Creating vector time with 394271 elements.
Creating vector dissolvedO2 with 394271 elements.
Creating vector time with 394271 elements.
Creating vector salinity with 394271 elements.
Creating vector time with 394271 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/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/2019/2019276/2019.276.02/ctdDriver2.nc')
Creating vector time with 394273 elements.
Creating vector conductivity with 394273 elements.
Creating vector time with 394273 elements.
Creating vector temperature with 394273 elements.
Creating vector time with 394273 elements.
Creating vector cond_frequency with 394273 elements.
Creating vector time with 394273 elements.
Creating vector temp_frequency with 394273 elements.
Creating vector time with 394273 elements.
Creating vector flow2 with 394273 elements.
Creating vector time with 394273 elements.
Creating vector spare with 394273 elements.
Creating vector time with 394273 elements.
Creating vector salinity with 394273 elements.
Creating vector time with 394273 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/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/2019/2019276/2019.276.02/isuslog.nc')
Creating vector time with 78163 elements.
Creating vector isusNitrate with 78163 elements.
Creating vector time with 78163 elements.
Creating vector isusTemp with 78163 elements.
Creating vector time with 78163 elements.
Creating vector isusQuality with 78163 elements.
Creating vector time with 78163 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/isuslog.nc');
Total lag applied to nitrate = 6 seconds
 
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/2019/2019276/2019.276.02/biolume.nc')
Creating vector time with 96957 elements.
Creating vector rrr with 96957 elements.
Creating vector time with 96957 elements.
Creating vector cal_striing with 96957 elements.
Creating vector time with 96957 elements.
Creating vector avg_biolume with 96957 elements.
Creating vector time with 96957 elements.
Creating vector pump with 96957 elements.
Creating vector time with 96957 elements.
Creating vector system_voltage with 96957 elements.
Creating vector time with 96957 elements.
Creating vector flow with 96957 elements.
Creating vector time with 96957 elements.
Creating vector HV with 96957 elements.
Creating vector time with 96957 elements.
Creating vector reserved with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_0 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_1 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_2 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_3 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_4 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_5 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_6 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_7 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_8 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_9 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_10 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_11 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_12 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_13 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_14 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_15 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_16 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_17 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_18 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_19 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_20 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_21 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_22 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_23 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_24 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_25 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_26 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_27 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_28 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_29 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_30 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_31 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_32 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_33 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_34 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_35 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_36 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_37 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_38 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_39 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_40 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_41 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_42 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_43 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_44 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_45 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_46 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_47 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_48 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_49 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_50 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_51 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_52 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_53 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_54 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_55 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_56 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_57 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_58 with 96957 elements.
Creating vector time with 96957 elements.
Creating vector raw_59 with 96957 elements.
Creating vector time with 96957 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/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/2019/2019276/2019.276.02/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (9386 x 994) with 9329684 elements.
Creating vector time with 9386 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (9386 x 994) with 9329684 elements.
Creating vector time with 9386 elements.
Creating vector bin with 994 elements.
Creating matrix countList (9386 x 994) with 9329684 elements.
Creating vector time with 9386 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 9386 elements.
Creating vector time with 9386 elements.
Creating vector transCount with 9386 elements.
Creating vector time with 9386 elements.
Creating vector nonTransCount with 9386 elements.
Creating vector time with 9386 elements.
Creating vector ai_mean with 9386 elements.
Creating vector time with 9386 elements.
Creating vector ai_min with 9386 elements.
Creating vector time with 9386 elements.
Creating vector ai_max with 9386 elements.
Creating vector time with 9386 elements.
Creating vector ai_std with 9386 elements.
Creating vector time with 9386 elements.
Creating vector esd_mean with 9386 elements.
Creating vector time with 9386 elements.
Creating vector esd_min with 9386 elements.
Creating vector time with 9386 elements.
Creating vector esd_max with 9386 elements.
Creating vector time with 9386 elements.
Creating vector esd_std with 9386 elements.
Creating vector time with 9386 elements.
Creating vector countSum with 9386 elements.
Creating vector time with 9386 elements.
Creating vector snapshot with 9386 elements.
Creating vector time with 9386 elements.
Creating vector threshold with 9386 elements.
Creating vector time with 9386 elements.
Creating vector sampleCount with 9386 elements.
Creating vector time with 9386 elements.
Creating vector flowCount with 9386 elements.
Creating vector time with 9386 elements.
Creating vector flowTime with 9386 elements.
Creating vector time with 9386 elements.
Creating vector bufferStatus with 9386 elements.
Creating vector time with 9386 elements.
Creating vector laserLevel with 9386 elements.
Creating vector time with 9386 elements.
Creating vector counter with 9386 elements.
Creating vector time with 9386 elements.
Creating vector counterPeriod with 9386 elements.
Creating vector time with 9386 elements.
Creating vector laserControl with 9386 elements.
Creating vector time with 9386 elements.
Creating vector countUnknownFrameCharacter with 9386 elements.
Creating vector time with 9386 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 9386 elements.
Creating vector time with 9386 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 9386 elements.
Creating vector time with 9386 elements.
Creating vector flowSpeed with 9386 elements.
Creating vector time with 9386 elements.
Creating vector countShortLFrameError with 9386 elements.
Creating vector time with 9386 elements.
Creating vector countGarbledLFrame with 9386 elements.
Creating vector time with 9386 elements.
Creating vector cFrameEsecs with 9386 elements.
Creating vector time with 9386 elements.
Creating vector correctedSampleCountList with 9386 elements.
Creating vector time with 9386 elements.
Creating vector time with 9386 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019276/2019.276.02/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019.276.02.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_2019.276.02.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 29 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_2019_276_02_276_02_nav_adjust.png
[Warning: P-file /mbari/matlab/toolbox/matlab/imagesci/imformats.p is older than
MATLAB file /mbari/matlab/toolbox/matlab/imagesci/imformats.m.
/mbari/matlab/toolbox/matlab/imagesci/imformats.p may be obsolete and may need
to be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In imwrite>parse_inputs (line 624)
  In imwrite (line 440)
  In matlab.graphics.internal.mlprintjob/writeRaster
  In printingGenerateOutput
  In alternatePrintPath
  In print (line 82)
  In create_data_products (line 98)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 257)] 
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02.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 = 250 Gridding with nix = 750, 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
   BL
   BLflow
   LOPC
     count
     transCount
     nonTransCount
     LCcount
 
Masking and filtering with median filter of size 5...
  cvarname = gT
  cvarname = gS
  cvarname = gO
  cvarname = 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 466354 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 466354 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 120672 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 = 25477.8106 since 1/1/1950
Looking for end   days = 25478.9513
sIndx = 
eIndx = 
Met data goes from 20017.6042 to 25054.7292
No SWR data loaded from URL.
Executing: /bin/rm -f ../results/2019276_GulperTimes.txt && touch ../results/2019276_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/2019/2019276/2019.276.02/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2019/2019276/2019.276.02/syslog -startEsecs 1570130833.2756 -surveyName Dorado389_2019_276_02_276_02 >> ../results/2019276_GulperTimes.txt
Executing: removeGulpDups.py ../results/2019276_GulperTimes.txt
Bottle: 0 Time: 1570178734.4476 Depth: 200.0358 Dist: 59.586
Bottle: 1 Time: 1570178854.6494 Depth: 149.9426 Dist: 59.6958
Bottle: 2 Time: 1570178963.0419 Depth: 99.9232 Dist: 59.8008
Bottle: 3 Time: 1570179071.4445 Depth: 49.9569 Dist: 59.9029
Bottle: 4 Time: 1570179134.4502 Depth: 24.9083 Dist: 59.9489
Bottle: 5 Time: 1570182421.4514 Depth: 200.0208 Dist: 63.6986
Bottle: 6 Time: 1570182542.4531 Depth: 149.9849 Dist: 63.7957
Bottle: 7 Time: 1570182651.2556 Depth: 99.9698 Dist: 63.8809
Bottle: 8 Time: 1570182760.6481 Depth: 49.9201 Dist: 63.9765
Bottle: 9 Time: 1570182818.4542 Depth: 24.9807 Dist: 64.0399
Bottle: 10 Time: 1570186001.4688 Depth: 200.0093 Dist: 67.75
Bottle: 11 Time: 1570186120.7407 Depth: 149.7059 Dist: 67.8502
Bottle: 12 Time: 1570186232.0631 Depth: 99.9962 Dist: 67.949
Bottle: 13 Time: 1570186342.4655 Depth: 49.9318 Dist: 68.0461
Bottle: 14 Time: 1570186403.2613 Depth: 24.9659 Dist: 68.0966
Bottle: 15 Time: 1570190056.0603 Depth: 200.0242 Dist: 72.5268
Bottle: 16 Time: 1570190174.0622 Depth: 149.9894 Dist: 72.6295
Bottle: 17 Time: 1570190283.4647 Depth: 99.9948 Dist: 72.7245
Bottle: 18 Time: 1570190393.6672 Depth: 49.9903 Dist: 72.8362
Bottle: 19 Time: 1570190453.6631 Depth: 24.9176 Dist: 72.9051
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_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 '

[Warning: P-file /mbari/matlab/toolbox/matlab/imagesci/imread.p is older than
MATLAB file /mbari/matlab/toolbox/matlab/imagesci/imread.m.
/mbari/matlab/toolbox/matlab/imagesci/imread.p may be obsolete and may need to
be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In plot_sections (line 782)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 257)] 
[Warning: P-file /mbari/matlab/toolbox/matlab/imagesci/private/imjpginfo.p is
older than MATLAB file
/mbari/matlab/toolbox/matlab/imagesci/private/imjpginfo.m.
/mbari/matlab/toolbox/matlab/imagesci/private/imjpginfo.p may be obsolete and
may need to be regenerated.
Type "help pcode" for information about generating P-files.] 
[> In readjpg (line 7)
  In imread
  In imread
  In plot_sections (line 782)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 257)] 
2Column contouring gridded variable gD
2Column contouring gridded variable gT
2Column contouring gridded variable gS
2Column contouring gridded variable gN
2Column contouring gridded variable gO
2Column contouring gridded variable gB420
2Column contouring gridded variable gB700
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Did not add swr plot to the image.
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_2column.png
Elapsed time to save image: 13 seconds
Biolume contouring gridded variable gD
Biolume contouring gridded variable gT
Biolume contouring gridded variable gS
Biolume contouring gridded variable gN
Biolume contouring gridded variable gO
Biolume contouring gridded variable gB420
Biolume contouring gridded variable gB700
Biolume contouring gridded variable gF
Biolume contouring gridded variable gBL
SWR image not added to the plot.
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_biolume.png
Elapsed time to save image: 72 seconds
2Column contouring gridded variable gLOPCcount
2Column contouring gridded variable gLOPCtransCount
2Column contouring gridded variable gLOPCnonTransCount
2Column contouring gridded variable gLOPCLCcount
2Column contouring gridded variable gT
2Column contouring gridded variable gB420
2Column contouring gridded variable gB700
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Did not add swr plot to the image.
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_lopc.png
Elapsed time to save image: 25 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_2019_276_02_276_02_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_2column.png...
Copied to /mbari/AUVCTD/surveys/2019/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_biolume.png...
Copied to /mbari/AUVCTD/surveys/2019/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_lopc.png...
Copied to /mbari/AUVCTD/surveys/2019/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2019/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2019/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2019/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
1 NaNs found in bbpBlue.  Interpolating anyway.
10 NaNs found in bbpRed.  Interpolating anyway.
1 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 4261 NaN values in array of lon that is 78116 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 73855 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 73855 are not equal to number of Lat lon points = 78116
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/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02.txt
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02.txt...
Copied to /mbari/AUVCTD/surveys/2019/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2019/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
1 NaNs found in bbpBlue.  Interpolating anyway.
10 NaNs found in bbpRed.  Interpolating anyway.
1 NaNs found in flRed_uncorr.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_decim.nc...
Copied to /mbari/AUVCTD/surveys/2019/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_2019_276_02_276_02.nc...
Copied to /mbari/AUVCTD/surveys/2019/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2019/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_276_02_276_02.mat...
Copied to /mbari/AUVCTD/surveys/2019/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2019_276_02_276_02 processed" mccann@mbari.org < mail_Dorado389_2019_276_02_276_02.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019.276.02.mat
Processing time: 71 seconds