Execution of AUVprocess_main version 1.88 at 2020-09-02T21:14:21Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2020, ['245.00';'246.01'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1')
 
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Processing data from SSDS via DODS server
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Processing AUV mission: 2020.245.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/
Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
Processing DVL navigation data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/navigation.nc')
Creating vector time with 115204 elements.
Creating vector mPos_x with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mPos_y with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mDepth with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mGpsNorth with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mGpsEast with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mGpsValid with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mPhi with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mTheta with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mPsi with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mOmega_x with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mOmega_y with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mOmega_z with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mPsaRange with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mAltitude with 115204 elements.
Creating vector time with 115204 elements.
Creating vector multibeamAltitude with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mDvlAltitude with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mEchoAltitude with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mEchoHorizRange with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mEchoAltitudeLast with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mEchoHorizRangeLast with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mEchoNumOfPings with 115204 elements.
Creating vector time with 115204 elements.
Creating vector nadirCnts with 115204 elements.
Creating vector time with 115204 elements.
Creating vector obstacleCnts with 115204 elements.
Creating vector time with 115204 elements.
Creating vector nGoodNadirBeams with 115204 elements.
Creating vector time with 115204 elements.
Creating vector medianNadirBeamNo with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mWaterSpeed with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mDvlValid with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mDvlNewData with 115204 elements.
Creating vector time with 115204 elements.
Creating vector mDeltaT with 115204 elements.
Creating vector time with 115204 elements.
Creating vector nfix with 115204 elements.
Creating vector time with 115204 elements.
Creating vector efix with 115204 elements.
Creating vector time with 115204 elements.
Creating vector filter_north with 115204 elements.
Creating vector time with 115204 elements.
Creating vector filter_east with 115204 elements.
Creating vector time with 115204 elements.
Creating vector filter_depth with 115204 elements.
Creating vector time with 115204 elements.
Creating vector north_current with 115204 elements.
Creating vector time with 115204 elements.
Creating vector east_current with 115204 elements.
Creating vector time with 115204 elements.
Creating vector speed_bias with 115204 elements.
Creating vector time with 115204 elements.
Creating vector heading_bias with 115204 elements.
Creating vector time with 115204 elements.
Creating vector latitude with 115204 elements.
Creating vector time with 115204 elements.
Creating vector longitude with 115204 elements.
Creating vector time with 115204 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/navigation.nc');
processNav(): median of positive valued depths = 34.8467
processNav(): Finding depths less than 243.9272 and times > 0
processNav(): length(Nav.depth) = 115204
processNav(): length(gindx)     = 115204
 
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/2020/2020245/2020.245.00/gps.nc')
Creating vector time with 8457 elements.
Creating vector hours with 8457 elements.
Creating vector time with 8457 elements.
Creating vector minutes with 8457 elements.
Creating vector time with 8457 elements.
Creating vector seconds with 8457 elements.
Creating vector time with 8457 elements.
Creating vector centiSeconds with 8457 elements.
Creating vector time with 8457 elements.
Creating vector latitude with 8457 elements.
Creating vector time with 8457 elements.
Creating vector longitude with 8457 elements.
Creating vector time with 8457 elements.
Creating vector quality with 8457 elements.
Creating vector time with 8457 elements.
Creating vector numberOfSatellites with 8457 elements.
Creating vector time with 8457 elements.
Creating vector hdop with 8457 elements.
Creating vector time with 8457 elements.
Creating vector antennaHeight with 8457 elements.
Creating vector time with 8457 elements.
Creating vector geoHeight with 8457 elements.
Creating vector time with 8457 elements.
Creating vector dgpsDataAge with 8457 elements.
Creating vector time with 8457 elements.
Creating vector dgpsRSID with 8457 elements.
Creating vector time with 8457 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/gps.nc');
 
Processing depth data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/parosci.nc')
Creating vector time with 229655 elements.
Creating vector depth with 229655 elements.
Creating vector time with 229655 elements.
Creating vector temp with 229655 elements.
Creating vector time with 229655 elements.
Creating vector pressure with 229655 elements.
Creating vector time with 229655 elements.
Creating vector temp_period with 229655 elements.
Creating vector time with 229655 elements.
Creating vector pres_period with 229655 elements.
Creating vector time with 229655 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.21079 max(Depth.data) = 202.2825
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.21079 max(Depth.data) = 202.2825
 
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/2020/2020245/2020.245.00/hydroscatlog.nc')
Creating vector time with 92253 elements.
Creating vector Seconds with 92253 elements.
Creating vector time with 92253 elements.
Creating vector HundrethsOfSeconds with 92253 elements.
Creating vector time with 92253 elements.
Creating vector Snorm1 with 92253 elements.
Creating vector time with 92253 elements.
Creating vector Snorm2 with 92253 elements.
Creating vector time with 92253 elements.
Creating vector Snorm3 with 92253 elements.
Creating vector time with 92253 elements.
Creating vector Gain_Status_1 with 92253 elements.
Creating vector time with 92253 elements.
Creating vector Gain_Status_2 with 92253 elements.
Creating vector time with 92253 elements.
Creating vector Gain_Status_3 with 92253 elements.
Creating vector time with 92253 elements.
Creating vector RawDepthValue with 92253 elements.
Creating vector time with 92253 elements.
Creating vector RawTempValue with 92253 elements.
Creating vector time with 92253 elements.
Creating vector Temperature with 92253 elements.
Creating vector time with 92253 elements.
Creating vector ErrorValue with 92253 elements.
Creating vector time with 92253 elements.
Creating vector bb470 with 92253 elements.
Creating vector time with 92253 elements.
Creating vector bb676 with 92253 elements.
Creating vector time with 92253 elements.
Creating vector fl676u with 92253 elements.
Creating vector time with 92253 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/hydroscatlog.nc');
 
Processing CTD #1 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/ctdDriver.nc')
Creating vector time with 92145 elements.
Creating vector conductivity with 92145 elements.
Creating vector time with 92145 elements.
Creating vector temperature with 92145 elements.
Creating vector time with 92145 elements.
Creating vector cond_frequency with 92145 elements.
Creating vector time with 92145 elements.
Creating vector temp_frequency with 92145 elements.
Creating vector time with 92145 elements.
Creating vector spare with 92145 elements.
Creating vector time with 92145 elements.
Creating vector humidity with 92145 elements.
Creating vector time with 92145 elements.
Creating vector flow1 with 92145 elements.
Creating vector time with 92145 elements.
Creating vector CDOM with 92145 elements.
Creating vector time with 92145 elements.
Creating vector dissolvedO2 with 92145 elements.
Creating vector time with 92145 elements.
Creating vector salinity with 92145 elements.
Creating vector time with 92145 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/ctdDriver.cfg
Oxygen calibration loaded from CTD config file (current method)
Using constant flow rate offset for oxygen...
 
Processing CTD #2 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/ctdDriver2.nc')
Creating vector time with 92211 elements.
Creating vector conductivity with 92211 elements.
Creating vector time with 92211 elements.
Creating vector temperature with 92211 elements.
Creating vector time with 92211 elements.
Creating vector cond_frequency with 92211 elements.
Creating vector time with 92211 elements.
Creating vector temp_frequency with 92211 elements.
Creating vector time with 92211 elements.
Creating vector flow2 with 92211 elements.
Creating vector time with 92211 elements.
Creating vector par with 92211 elements.
Creating vector time with 92211 elements.
Creating vector spare with 92211 elements.
Creating vector time with 92211 elements.
Creating vector salinity with 92211 elements.
Creating vector time with 92211 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/ctdDriver2.cfg
 
Processing ISUS data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/isuslog.nc')
Creating vector time with 17973 elements.
Creating vector isusNitrate with 17973 elements.
Creating vector time with 17973 elements.
Creating vector isusTemp with 17973 elements.
Creating vector time with 17973 elements.
Creating vector isusQuality with 17973 elements.
Creating vector time with 17973 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/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/2020/2020245/2020.245.00/biolume.nc')
Creating vector time with 22690 elements.
Creating vector rrr with 22690 elements.
Creating vector time with 22690 elements.
Creating vector cal_striing with 22690 elements.
Creating vector time with 22690 elements.
Creating vector avg_biolume with 22690 elements.
Creating vector time with 22690 elements.
Creating vector pump with 22690 elements.
Creating vector time with 22690 elements.
Creating vector system_voltage with 22690 elements.
Creating vector time with 22690 elements.
Creating vector flow with 22690 elements.
Creating vector time with 22690 elements.
Creating vector HV with 22690 elements.
Creating vector time with 22690 elements.
Creating vector reserved with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_0 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_1 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_2 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_3 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_4 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_5 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_6 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_7 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_8 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_9 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_10 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_11 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_12 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_13 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_14 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_15 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_16 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_17 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_18 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_19 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_20 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_21 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_22 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_23 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_24 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_25 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_26 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_27 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_28 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_29 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_30 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_31 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_32 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_33 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_34 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_35 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_36 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_37 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_38 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_39 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_40 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_41 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_42 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_43 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_44 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_45 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_46 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_47 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_48 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_49 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_50 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_51 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_52 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_53 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_54 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_55 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_56 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_57 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_58 with 22690 elements.
Creating vector time with 22690 elements.
Creating vector raw_59 with 22690 elements.
Creating vector time with 22690 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (1904 x 994) with 1892576 elements.
Creating vector time with 1904 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (1904 x 994) with 1892576 elements.
Creating vector time with 1904 elements.
Creating vector bin with 994 elements.
Creating matrix countList (1904 x 994) with 1892576 elements.
Creating vector time with 1904 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 1904 elements.
Creating vector time with 1904 elements.
Creating vector transCount with 1904 elements.
Creating vector time with 1904 elements.
Creating vector nonTransCount with 1904 elements.
Creating vector time with 1904 elements.
Creating vector ai_mean with 1904 elements.
Creating vector time with 1904 elements.
Creating vector ai_min with 1904 elements.
Creating vector time with 1904 elements.
Creating vector ai_max with 1904 elements.
Creating vector time with 1904 elements.
Creating vector ai_std with 1904 elements.
Creating vector time with 1904 elements.
Creating vector esd_mean with 1904 elements.
Creating vector time with 1904 elements.
Creating vector esd_min with 1904 elements.
Creating vector time with 1904 elements.
Creating vector esd_max with 1904 elements.
Creating vector time with 1904 elements.
Creating vector esd_std with 1904 elements.
Creating vector time with 1904 elements.
Creating vector countSum with 1904 elements.
Creating vector time with 1904 elements.
Creating vector snapshot with 1904 elements.
Creating vector time with 1904 elements.
Creating vector threshold with 1904 elements.
Creating vector time with 1904 elements.
Creating vector sampleCount with 1904 elements.
Creating vector time with 1904 elements.
Creating vector flowCount with 1904 elements.
Creating vector time with 1904 elements.
Creating vector flowTime with 1904 elements.
Creating vector time with 1904 elements.
Creating vector bufferStatus with 1904 elements.
Creating vector time with 1904 elements.
Creating vector laserLevel with 1904 elements.
Creating vector time with 1904 elements.
Creating vector counter with 1904 elements.
Creating vector time with 1904 elements.
Creating vector counterPeriod with 1904 elements.
Creating vector time with 1904 elements.
Creating vector laserControl with 1904 elements.
Creating vector time with 1904 elements.
Creating vector countUnknownFrameCharacter with 1904 elements.
Creating vector time with 1904 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 1904 elements.
Creating vector time with 1904 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 1904 elements.
Creating vector time with 1904 elements.
Creating vector flowSpeed with 1904 elements.
Creating vector time with 1904 elements.
Creating vector countShortLFrameError with 1904 elements.
Creating vector time with 1904 elements.
Creating vector countGarbledLFrame with 1904 elements.
Creating vector time with 1904 elements.
Creating vector cFrameEsecs with 1904 elements.
Creating vector time with 1904 elements.
Creating vector correctedSampleCountList with 1904 elements.
Creating vector time with 1904 elements.
Creating vector time with 1904 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020245/2020.245.00/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.245.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2020.246.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/
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/2020/2020246/2020.246.01/navigation.nc')
Creating vector time with 259323 elements.
Creating vector mPos_x with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mPos_y with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mDepth with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mGpsNorth with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mGpsEast with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mGpsValid with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mPhi with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mTheta with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mPsi with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mOmega_x with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mOmega_y with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mOmega_z with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mPsaRange with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mAltitude with 259323 elements.
Creating vector time with 259323 elements.
Creating vector multibeamAltitude with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mDvlAltitude with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mEchoAltitude with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mEchoHorizRange with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mEchoAltitudeLast with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mEchoHorizRangeLast with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mEchoNumOfPings with 259323 elements.
Creating vector time with 259323 elements.
Creating vector nadirCnts with 259323 elements.
Creating vector time with 259323 elements.
Creating vector obstacleCnts with 259323 elements.
Creating vector time with 259323 elements.
Creating vector nGoodNadirBeams with 259323 elements.
Creating vector time with 259323 elements.
Creating vector medianNadirBeamNo with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mWaterSpeed with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mDvlValid with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mDvlNewData with 259323 elements.
Creating vector time with 259323 elements.
Creating vector mDeltaT with 259323 elements.
Creating vector time with 259323 elements.
Creating vector nfix with 259323 elements.
Creating vector time with 259323 elements.
Creating vector efix with 259323 elements.
Creating vector time with 259323 elements.
Creating vector filter_north with 259323 elements.
Creating vector time with 259323 elements.
Creating vector filter_east with 259323 elements.
Creating vector time with 259323 elements.
Creating vector filter_depth with 259323 elements.
Creating vector time with 259323 elements.
Creating vector north_current with 259323 elements.
Creating vector time with 259323 elements.
Creating vector east_current with 259323 elements.
Creating vector time with 259323 elements.
Creating vector speed_bias with 259323 elements.
Creating vector time with 259323 elements.
Creating vector heading_bias with 259323 elements.
Creating vector time with 259323 elements.
Creating vector latitude with 259323 elements.
Creating vector time with 259323 elements.
Creating vector longitude with 259323 elements.
Creating vector time with 259323 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/navigation.nc');
processNav(): median of positive valued depths = 33.8371
processNav(): Finding depths less than 236.8597 and times > 0
processNav(): length(Nav.depth) = 259323
processNav(): length(gindx)     = 259323
 
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/2020/2020246/2020.246.01/gps.nc')
Creating vector time with 16806 elements.
Creating vector hours with 16806 elements.
Creating vector time with 16806 elements.
Creating vector minutes with 16806 elements.
Creating vector time with 16806 elements.
Creating vector seconds with 16806 elements.
Creating vector time with 16806 elements.
Creating vector centiSeconds with 16806 elements.
Creating vector time with 16806 elements.
Creating vector latitude with 16806 elements.
Creating vector time with 16806 elements.
Creating vector longitude with 16806 elements.
Creating vector time with 16806 elements.
Creating vector quality with 16806 elements.
Creating vector time with 16806 elements.
Creating vector numberOfSatellites with 16806 elements.
Creating vector time with 16806 elements.
Creating vector hdop with 16806 elements.
Creating vector time with 16806 elements.
Creating vector antennaHeight with 16806 elements.
Creating vector time with 16806 elements.
Creating vector geoHeight with 16806 elements.
Creating vector time with 16806 elements.
Creating vector dgpsDataAge with 16806 elements.
Creating vector time with 16806 elements.
Creating vector dgpsRSID with 16806 elements.
Creating vector time with 16806 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/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/2020/2020246/2020.246.01/parosci.nc')
Creating vector time with 516549 elements.
Creating vector depth with 516549 elements.
Creating vector time with 516549 elements.
Creating vector temp with 516549 elements.
Creating vector time with 516549 elements.
Creating vector pressure with 516549 elements.
Creating vector time with 516549 elements.
Creating vector temp_period with 516549 elements.
Creating vector time with 516549 elements.
Creating vector pres_period with 516549 elements.
Creating vector time with 516549 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.18746 max(Depth.data) = 202.4721
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.18746 max(Depth.data) = 202.4721
 
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/2020/2020246/2020.246.01/hydroscatlog.nc')
Creating vector time with 207476 elements.
Creating vector Seconds with 207476 elements.
Creating vector time with 207476 elements.
Creating vector HundrethsOfSeconds with 207476 elements.
Creating vector time with 207476 elements.
Creating vector Snorm1 with 207476 elements.
Creating vector time with 207476 elements.
Creating vector Snorm2 with 207476 elements.
Creating vector time with 207476 elements.
Creating vector Snorm3 with 207476 elements.
Creating vector time with 207476 elements.
Creating vector Gain_Status_1 with 207476 elements.
Creating vector time with 207476 elements.
Creating vector Gain_Status_2 with 207476 elements.
Creating vector time with 207476 elements.
Creating vector Gain_Status_3 with 207476 elements.
Creating vector time with 207476 elements.
Creating vector RawDepthValue with 207476 elements.
Creating vector time with 207476 elements.
Creating vector RawTempValue with 207476 elements.
Creating vector time with 207476 elements.
Creating vector Temperature with 207476 elements.
Creating vector time with 207476 elements.
Creating vector ErrorValue with 207476 elements.
Creating vector time with 207476 elements.
Creating vector bb470 with 207476 elements.
Creating vector time with 207476 elements.
Creating vector bb676 with 207476 elements.
Creating vector time with 207476 elements.
Creating vector fl676u with 207476 elements.
Creating vector time with 207476 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/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/2020/2020246/2020.246.01/ctdDriver.nc')
Creating vector time with 207547 elements.
Creating vector conductivity with 207547 elements.
Creating vector time with 207547 elements.
Creating vector temperature with 207547 elements.
Creating vector time with 207547 elements.
Creating vector cond_frequency with 207547 elements.
Creating vector time with 207547 elements.
Creating vector temp_frequency with 207547 elements.
Creating vector time with 207547 elements.
Creating vector spare with 207547 elements.
Creating vector time with 207547 elements.
Creating vector humidity with 207547 elements.
Creating vector time with 207547 elements.
Creating vector flow1 with 207547 elements.
Creating vector time with 207547 elements.
Creating vector CDOM with 207547 elements.
Creating vector time with 207547 elements.
Creating vector dissolvedO2 with 207547 elements.
Creating vector time with 207547 elements.
Creating vector salinity with 207547 elements.
Creating vector time with 207547 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/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/2020/2020246/2020.246.01/ctdDriver2.nc')
Creating vector time with 207546 elements.
Creating vector conductivity with 207546 elements.
Creating vector time with 207546 elements.
Creating vector temperature with 207546 elements.
Creating vector time with 207546 elements.
Creating vector cond_frequency with 207546 elements.
Creating vector time with 207546 elements.
Creating vector temp_frequency with 207546 elements.
Creating vector time with 207546 elements.
Creating vector flow2 with 207546 elements.
Creating vector time with 207546 elements.
Creating vector par with 207546 elements.
Creating vector time with 207546 elements.
Creating vector spare with 207546 elements.
Creating vector time with 207546 elements.
Creating vector salinity with 207546 elements.
Creating vector time with 207546 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/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/2020/2020246/2020.246.01/isuslog.nc')
Creating vector time with 40495 elements.
Creating vector isusNitrate with 40495 elements.
Creating vector time with 40495 elements.
Creating vector isusTemp with 40495 elements.
Creating vector time with 40495 elements.
Creating vector isusQuality with 40495 elements.
Creating vector time with 40495 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/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/2020/2020246/2020.246.01/biolume.nc')
Creating vector time with 51030 elements.
Creating vector rrr with 51030 elements.
Creating vector time with 51030 elements.
Creating vector cal_striing with 51030 elements.
Creating vector time with 51030 elements.
Creating vector avg_biolume with 51030 elements.
Creating vector time with 51030 elements.
Creating vector pump with 51030 elements.
Creating vector time with 51030 elements.
Creating vector system_voltage with 51030 elements.
Creating vector time with 51030 elements.
Creating vector flow with 51030 elements.
Creating vector time with 51030 elements.
Creating vector HV with 51030 elements.
Creating vector time with 51030 elements.
Creating vector reserved with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_0 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_1 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_2 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_3 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_4 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_5 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_6 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_7 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_8 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_9 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_10 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_11 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_12 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_13 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_14 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_15 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_16 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_17 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_18 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_19 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_20 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_21 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_22 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_23 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_24 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_25 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_26 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_27 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_28 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_29 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_30 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_31 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_32 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_33 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_34 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_35 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_36 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_37 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_38 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_39 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_40 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_41 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_42 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_43 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_44 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_45 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_46 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_47 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_48 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_49 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_50 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_51 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_52 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_53 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_54 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_55 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_56 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_57 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_58 with 51030 elements.
Creating vector time with 51030 elements.
Creating vector raw_59 with 51030 elements.
Creating vector time with 51030 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/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/2020/2020246/2020.246.01/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (4441 x 994) with 4414354 elements.
Creating vector time with 4441 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (4441 x 994) with 4414354 elements.
Creating vector time with 4441 elements.
Creating vector bin with 994 elements.
Creating matrix countList (4441 x 994) with 4414354 elements.
Creating vector time with 4441 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 4441 elements.
Creating vector time with 4441 elements.
Creating vector transCount with 4441 elements.
Creating vector time with 4441 elements.
Creating vector nonTransCount with 4441 elements.
Creating vector time with 4441 elements.
Creating vector ai_mean with 4441 elements.
Creating vector time with 4441 elements.
Creating vector ai_min with 4441 elements.
Creating vector time with 4441 elements.
Creating vector ai_max with 4441 elements.
Creating vector time with 4441 elements.
Creating vector ai_std with 4441 elements.
Creating vector time with 4441 elements.
Creating vector esd_mean with 4441 elements.
Creating vector time with 4441 elements.
Creating vector esd_min with 4441 elements.
Creating vector time with 4441 elements.
Creating vector esd_max with 4441 elements.
Creating vector time with 4441 elements.
Creating vector esd_std with 4441 elements.
Creating vector time with 4441 elements.
Creating vector countSum with 4441 elements.
Creating vector time with 4441 elements.
Creating vector snapshot with 4441 elements.
Creating vector time with 4441 elements.
Creating vector threshold with 4441 elements.
Creating vector time with 4441 elements.
Creating vector sampleCount with 4441 elements.
Creating vector time with 4441 elements.
Creating vector flowCount with 4441 elements.
Creating vector time with 4441 elements.
Creating vector flowTime with 4441 elements.
Creating vector time with 4441 elements.
Creating vector bufferStatus with 4441 elements.
Creating vector time with 4441 elements.
Creating vector laserLevel with 4441 elements.
Creating vector time with 4441 elements.
Creating vector counter with 4441 elements.
Creating vector time with 4441 elements.
Creating vector counterPeriod with 4441 elements.
Creating vector time with 4441 elements.
Creating vector laserControl with 4441 elements.
Creating vector time with 4441 elements.
Creating vector countUnknownFrameCharacter with 4441 elements.
Creating vector time with 4441 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 4441 elements.
Creating vector time with 4441 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 4441 elements.
Creating vector time with 4441 elements.
Creating vector flowSpeed with 4441 elements.
Creating vector time with 4441 elements.
Creating vector countShortLFrameError with 4441 elements.
Creating vector time with 4441 elements.
Creating vector countGarbledLFrame with 4441 elements.
Creating vector time with 4441 elements.
Creating vector cFrameEsecs with 4441 elements.
Creating vector time with 4441 elements.
Creating vector correctedSampleCountList with 4441 elements.
Creating vector time with 4441 elements.
Creating vector time with 4441 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020246/2020.246.01/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.246.01.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.cvs/src/matlab/doradosdp/results/Dorado389_2020.245.00.mat
Reading: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.246.01.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.cvs/src/matlab/doradosdp/results/Dorado389_2020_245_00_246_01_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_245_00_246_01.mat
Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_245_00_246_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 = 312 Gridding with nix = 936, iZ = 402
Using mean boxcar filter of vector...
Using mean boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Gridding...
   T
   S
   O
Using median boxcar filter of vector...
Using median boxcar filter of vector...
Using median boxcar filter of vector...
   bbp420
   bbp700
   fl700_uncorr
   N
   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 302707 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 302707 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 = 25811.8125 since 1/1/1950
Looking for end   days = 25812.693
sIndx = 
eIndx = 
Met data goes from 20017.6042 to 25054.7292
No SWR data loaded from URL.
Executing: /bin/rm -f ../results/2020245_GulperTimes.txt && touch ../results/2020245_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/2020/2020245/2020.245.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2020/2020245/2020.245.00/syslog -startEsecs 1599012808.6897 -surveyName Dorado389_2020_245_00_246_01 >> ../results/2020245_GulperTimes.txt
Executing: removeGulpDups.py ../results/2020245_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/2020/2020246/2020.246.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2020/2020246/2020.246.01/syslog -startEsecs 1599012808.6897 -surveyName Dorado389_2020_245_00_246_01 >> ../results/2020245_GulperTimes.txt
Executing: removeGulpDups.py ../results/2020245_GulperTimes.txt
Bottle: 0 Time: 1599016954.8857 Depth: 20.105 Dist: 23.6026
Bottle: 1 Time: 1599017083.0869 Depth: 68.8668 Dist: 23.7615
Bottle: 2 Time: 1599017187.8897 Depth: 25.632 Dist: 23.8914
Bottle: 3 Time: 1599017291.6826 Depth: 18.6563 Dist: 24.0103
Bottle: 4 Time: 1599017333.4897 Depth: 33.9253 Dist: 24.0553
Bottle: 5 Time: 1599021586.2884 Depth: 44.2445 Dist: 29.0275
Bottle: 6 Time: 1599025765.2821 Depth: 46.4826 Dist: 34.0322
Bottle: 7 Time: 1599029877.2904 Depth: 55.1344 Dist: 39.1939
Bottle: 8 Time: 1599033903.4846 Depth: 62.5867 Dist: 43.1261
Bottle: 12 Time: 1599030271.4834 Depth: 5.0154 Dist: 39.4222
Bottle: 13 Time: 1599035948.0845 Depth: 5.0569 Dist: 45.4497
Bottle: 14 Time: 1599039712.8866 Depth: 5.0113 Dist: 49.916
Bottle: 15 Time: 1599043385.885 Depth: 5.0077 Dist: 54.2954
Bottle: 16 Time: 1599046858.2871 Depth: 5.0394 Dist: 58.2943
Bottle 17 time is 300.6394 seconds greater than nearest time in (sub)section auvnav.fixTime vector.
Bottle 18 time is 3632.0311 seconds greater than nearest time in (sub)section auvnav.fixTime vector.
Bottle 19 time is 7075.0353 seconds greater than nearest time in (sub)section auvnav.fixTime vector.
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_245_00_246_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_2020_245_00_246_01_2column.png
Elapsed time to save image: 9 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_2020_245_00_246_01_biolume.png
Elapsed time to save image: 37 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_2020_245_00_246_01_lopc.png
Elapsed time to save image: 12 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_2020_245_00_246_01_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_245_00_246_01_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_245_00_246_01_2column.png...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_biolume.png...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_lopc.png...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2020/images/.  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_2020_245_00_246_01_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_245_00_246_01_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_245_00_246_01_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2020/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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_245_00_246_01_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_245_00_246_01_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_245_00_246_01_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_Optical_Backscatter_420_nm.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_245_00_246_01_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_245_00_246_01_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_245_00_246_01_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_245_00_246_01_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_245_00_246_01_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2020/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
Creating Dorado389_2020_245_00_246_01.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_245_00_246_01.kml...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_LOPC_Total_Count.kml'
not found.] 
[> In create_data_products (line 419)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 257)] 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_245_00_246_01.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
8 NaNs found in bbpBlue.  Interpolating anyway.
305 NaNs found in bbpRed.  Interpolating anyway.
62 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 11220 NaN values in array of lon that is 58468 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 47248 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 47248 are not equal to number of Lat lon points = 58468
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_2020_245_00_246_01.txt
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_245_00_246_01_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_245_00_246_01.txt...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2020/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
8 NaNs found in bbpBlue.  Interpolating anyway.
305 NaNs found in bbpRed.  Interpolating anyway.
62 NaNs found in flRed_uncorr.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_245_00_246_01_decim.nc...
Copied to /mbari/AUVCTD/surveys/2020/netcdf/.  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_2020_245_00_246_01.nc...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2020/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_2020_245_00_246_01.mat...
Copied to /mbari/AUVCTD/surveys/2020/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2020_245_00_246_01 processed" mccann@mbari.org < mail_Dorado389_2020_245_00_246_01.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.245.00.mat
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.246.01.mat
Processing time: 236 seconds