Execution of AUVprocess_main version 1.86 at 2018-06-02T04:01:31Z on elvis
Matlab command executed: 
   AUVprocess_main('DMOSeaTrials', 2003, ['317.02';'317.03';'317.04'], '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: 2003.317.02
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/
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/2003/2003317/2003.317.02/navigation.nc')
Creating vector time with 6550 elements.
Creating vector mPos_x with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mPos_y with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mDepth with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mGpsNorth with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mGpsEast with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mGpsValid with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mPhi with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mTheta with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mPsi with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mOmega_x with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mOmega_y with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mOmega_z with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mPsaRange with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mAltitude with 6550 elements.
Creating vector time with 6550 elements.
Creating vector mWaterSpeed with 6550 elements.
Creating vector time with 6550 elements.
Creating vector nfix with 6550 elements.
Creating vector time with 6550 elements.
Creating vector efix with 6550 elements.
Creating vector time with 6550 elements.
Creating vector filter_north with 6550 elements.
Creating vector time with 6550 elements.
Creating vector filter_east with 6550 elements.
Creating vector time with 6550 elements.
Creating vector filter_depth with 6550 elements.
Creating vector time with 6550 elements.
Creating vector north_current with 6550 elements.
Creating vector time with 6550 elements.
Creating vector east_current with 6550 elements.
Creating vector time with 6550 elements.
Creating vector speed_bias with 6550 elements.
Creating vector time with 6550 elements.
Creating vector heading_bias with 6550 elements.
Creating vector time with 6550 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/navigation.nc');
processNav(): median of positive valued depths = 111.6098
processNav(): Finding depths less than 781.2683 and times > 0
processNav(): length(Nav.depth) = 6550
processNav(): length(gindx)     = 6550
 
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/2003/2003317/2003.317.02/gps.nc')
Creating vector time with 90 elements.
Creating vector UTCTime with 90 elements.
Creating vector time with 90 elements.
Creating vector latitude with 90 elements.
Creating vector time with 90 elements.
Creating vector longitude with 90 elements.
Creating vector time with 90 elements.
Creating vector quality with 90 elements.
Creating vector time with 90 elements.
Creating vector numberOfSatellites with 90 elements.
Creating vector time with 90 elements.
Creating vector hdop with 90 elements.
Creating vector time with 90 elements.
Creating vector antennaHeight with 90 elements.
Creating vector time with 90 elements.
Creating vector geoHeight with 90 elements.
Creating vector time with 90 elements.
Creating vector dgpsDataAge with 90 elements.
Creating vector time with 90 elements.
Creating vector dgpsRSID with 90 elements.
Creating vector time with 90 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/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/2003/2003317/2003.317.02/parosci.nc')
Creating vector time with 6655 elements.
Creating vector depth with 6655 elements.
Creating vector time with 6655 elements.
Creating vector temp with 6655 elements.
Creating vector time with 6655 elements.
Creating vector pressure with 6655 elements.
Creating vector time with 6655 elements.
Creating vector temp_period with 6655 elements.
Creating vector time with 6655 elements.
Creating vector pres_period with 6655 elements.
Creating vector time with 6655 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.3228 max(Depth.data) = 201.6481
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.3228 max(Depth.data) = 201.6481
 
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/2003/2003317/2003.317.02/hydroscatlog.nc')
Creating vector time with 5309 elements.
Creating vector Seconds with 5309 elements.
Creating vector time with 5309 elements.
Creating vector HundrethsOfSeconds with 5309 elements.
Creating vector time with 5309 elements.
Creating vector Snorm1 with 5309 elements.
Creating vector time with 5309 elements.
Creating vector Snorm2 with 5309 elements.
Creating vector time with 5309 elements.
Creating vector Snorm3 with 5309 elements.
Creating vector time with 5309 elements.
Creating vector Gain_Status_1 with 5309 elements.
Creating vector time with 5309 elements.
Creating vector Gain_Status_2 with 5309 elements.
Creating vector time with 5309 elements.
Creating vector Gain_Status_3 with 5309 elements.
Creating vector time with 5309 elements.
Creating vector RawDepthValue with 5309 elements.
Creating vector time with 5309 elements.
Creating vector RawTempValue with 5309 elements.
Creating vector time with 5309 elements.
Creating vector Temperature with 5309 elements.
Creating vector time with 5309 elements.
Creating vector ErrorValue with 5309 elements.
Creating vector time with 5309 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/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/2003/2003317/2003.317.02/ctdDriver.nc')
Creating vector time with 5246 elements.
Creating vector conductivity with 5246 elements.
Creating vector time with 5246 elements.
Creating vector temperature with 5246 elements.
Creating vector time with 5246 elements.
Creating vector cond_frequency with 5246 elements.
Creating vector time with 5246 elements.
Creating vector temp_frequency with 5246 elements.
Creating vector time with 5246 elements.
Creating vector spare with 5246 elements.
Creating vector time with 5246 elements.
Creating vector humidity with 5246 elements.
Creating vector time with 5246 elements.
Creating vector flow1 with 5246 elements.
Creating vector time with 5246 elements.
Creating vector OBS with 5246 elements.
Creating vector time with 5246 elements.
Creating vector dissolvedO2 with 5246 elements.
Creating vector time with 5246 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/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/2003/2003317/2003.317.02/ctdDriver2.nc')
Creating vector time with 5246 elements.
Creating vector conductivity with 5246 elements.
Creating vector time with 5246 elements.
Creating vector temperature with 5246 elements.
Creating vector time with 5246 elements.
Creating vector cond_frequency with 5246 elements.
Creating vector time with 5246 elements.
Creating vector temp_frequency with 5246 elements.
Creating vector time with 5246 elements.
Creating vector flow2 with 5246 elements.
Creating vector time with 5246 elements.
Creating vector spare with 5246 elements.
Creating vector time with 5246 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/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/2003/2003317/2003.317.02/isuslog.nc')
Creating vector time with 759 elements.
Creating vector isusNitrate with 759 elements.
Creating vector time with 759 elements.
Creating vector isusTemp with 759 elements.
Creating vector time with 759 elements.
Creating vector isusQuality with 759 elements.
Creating vector time with 759 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/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 75)
  In processBiolume (line 21)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
[Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 75)
  In processBiolume (line 22)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
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/2003/2003317/2003.317.02/lopc.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/lopc.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/lopc.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.02/lopc.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


*** Setting lopc structure to NaNs. *** 
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.317.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
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*************************************************************************
Processing AUV mission: 2003.317.03
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/
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/2003/2003317/2003.317.03/navigation.nc')
Creating vector time with 14082 elements.
Creating vector mPos_x with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mPos_y with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mDepth with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mGpsNorth with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mGpsEast with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mGpsValid with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mPhi with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mTheta with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mPsi with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mOmega_x with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mOmega_y with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mOmega_z with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mPsaRange with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mAltitude with 14082 elements.
Creating vector time with 14082 elements.
Creating vector mWaterSpeed with 14082 elements.
Creating vector time with 14082 elements.
Creating vector nfix with 14082 elements.
Creating vector time with 14082 elements.
Creating vector efix with 14082 elements.
Creating vector time with 14082 elements.
Creating vector filter_north with 14082 elements.
Creating vector time with 14082 elements.
Creating vector filter_east with 14082 elements.
Creating vector time with 14082 elements.
Creating vector filter_depth with 14082 elements.
Creating vector time with 14082 elements.
Creating vector north_current with 14082 elements.
Creating vector time with 14082 elements.
Creating vector east_current with 14082 elements.
Creating vector time with 14082 elements.
Creating vector speed_bias with 14082 elements.
Creating vector time with 14082 elements.
Creating vector heading_bias with 14082 elements.
Creating vector time with 14082 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/navigation.nc');
processNav(): median of positive valued depths = 263.3219
processNav(): Finding depths less than 1843.2533 and times > 0
processNav(): length(Nav.depth) = 14082
processNav(): length(gindx)     = 14082
 
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/2003/2003317/2003.317.03/gps.nc')
Creating vector time with 77 elements.
Creating vector UTCTime with 77 elements.
Creating vector time with 77 elements.
Creating vector latitude with 77 elements.
Creating vector time with 77 elements.
Creating vector longitude with 77 elements.
Creating vector time with 77 elements.
Creating vector quality with 77 elements.
Creating vector time with 77 elements.
Creating vector numberOfSatellites with 77 elements.
Creating vector time with 77 elements.
Creating vector hdop with 77 elements.
Creating vector time with 77 elements.
Creating vector antennaHeight with 77 elements.
Creating vector time with 77 elements.
Creating vector geoHeight with 77 elements.
Creating vector time with 77 elements.
Creating vector dgpsDataAge with 77 elements.
Creating vector time with 77 elements.
Creating vector dgpsRSID with 77 elements.
Creating vector time with 77 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/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/2003/2003317/2003.317.03/parosci.nc')
Creating vector time with 14187 elements.
Creating vector depth with 14187 elements.
Creating vector time with 14187 elements.
Creating vector temp with 14187 elements.
Creating vector time with 14187 elements.
Creating vector pressure with 14187 elements.
Creating vector time with 14187 elements.
Creating vector temp_period with 14187 elements.
Creating vector time with 14187 elements.
Creating vector pres_period with 14187 elements.
Creating vector time with 14187 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.39495 max(Depth.data) = 501.6505
Found 5883 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.39495 max(Depth.data) = 299.9958
 
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/2003/2003317/2003.317.03/hydroscatlog.nc')
Creating vector time with 11331 elements.
Creating vector Seconds with 11331 elements.
Creating vector time with 11331 elements.
Creating vector HundrethsOfSeconds with 11331 elements.
Creating vector time with 11331 elements.
Creating vector Snorm1 with 11331 elements.
Creating vector time with 11331 elements.
Creating vector Snorm2 with 11331 elements.
Creating vector time with 11331 elements.
Creating vector Snorm3 with 11331 elements.
Creating vector time with 11331 elements.
Creating vector Gain_Status_1 with 11331 elements.
Creating vector time with 11331 elements.
Creating vector Gain_Status_2 with 11331 elements.
Creating vector time with 11331 elements.
Creating vector Gain_Status_3 with 11331 elements.
Creating vector time with 11331 elements.
Creating vector RawDepthValue with 11331 elements.
Creating vector time with 11331 elements.
Creating vector RawTempValue with 11331 elements.
Creating vector time with 11331 elements.
Creating vector Temperature with 11331 elements.
Creating vector time with 11331 elements.
Creating vector ErrorValue with 11331 elements.
Creating vector time with 11331 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/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/2003/2003317/2003.317.03/ctdDriver.nc')
Creating vector time with 11272 elements.
Creating vector conductivity with 11272 elements.
Creating vector time with 11272 elements.
Creating vector temperature with 11272 elements.
Creating vector time with 11272 elements.
Creating vector cond_frequency with 11272 elements.
Creating vector time with 11272 elements.
Creating vector temp_frequency with 11272 elements.
Creating vector time with 11272 elements.
Creating vector spare with 11272 elements.
Creating vector time with 11272 elements.
Creating vector humidity with 11272 elements.
Creating vector time with 11272 elements.
Creating vector flow1 with 11272 elements.
Creating vector time with 11272 elements.
Creating vector OBS with 11272 elements.
Creating vector time with 11272 elements.
Creating vector dissolvedO2 with 11272 elements.
Creating vector time with 11272 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/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/2003/2003317/2003.317.03/ctdDriver2.nc')
Creating vector time with 11271 elements.
Creating vector conductivity with 11271 elements.
Creating vector time with 11271 elements.
Creating vector temperature with 11271 elements.
Creating vector time with 11271 elements.
Creating vector cond_frequency with 11271 elements.
Creating vector time with 11271 elements.
Creating vector temp_frequency with 11271 elements.
Creating vector time with 11271 elements.
Creating vector flow2 with 11271 elements.
Creating vector time with 11271 elements.
Creating vector spare with 11271 elements.
Creating vector time with 11271 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/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/2003/2003317/2003.317.03/isuslog.nc')
Creating vector time with 1672 elements.
Creating vector isusNitrate with 1672 elements.
Creating vector time with 1672 elements.
Creating vector isusTemp with 1672 elements.
Creating vector time with 1672 elements.
Creating vector isusQuality with 1672 elements.
Creating vector time with 1672 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/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 75)
  In processBiolume (line 21)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
[Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 75)
  In processBiolume (line 22)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
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/2003/2003317/2003.317.03/lopc.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/lopc.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/lopc.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.03/lopc.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


*** Setting lopc structure to NaNs. *** 
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.317.03.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2003.317.04
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/
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/2003/2003317/2003.317.04/navigation.nc')
Creating vector time with 26916 elements.
Creating vector mPos_x with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mPos_y with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mDepth with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mGpsNorth with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mGpsEast with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mGpsValid with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mPhi with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mTheta with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mPsi with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mOmega_x with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mOmega_y with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mOmega_z with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mPsaRange with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mAltitude with 26916 elements.
Creating vector time with 26916 elements.
Creating vector mWaterSpeed with 26916 elements.
Creating vector time with 26916 elements.
Creating vector nfix with 26916 elements.
Creating vector time with 26916 elements.
Creating vector efix with 26916 elements.
Creating vector time with 26916 elements.
Creating vector filter_north with 26916 elements.
Creating vector time with 26916 elements.
Creating vector filter_east with 26916 elements.
Creating vector time with 26916 elements.
Creating vector filter_depth with 26916 elements.
Creating vector time with 26916 elements.
Creating vector north_current with 26916 elements.
Creating vector time with 26916 elements.
Creating vector east_current with 26916 elements.
Creating vector time with 26916 elements.
Creating vector speed_bias with 26916 elements.
Creating vector time with 26916 elements.
Creating vector heading_bias with 26916 elements.
Creating vector time with 26916 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/navigation.nc');
processNav(): median of positive valued depths = 510.2916
processNav(): Finding depths less than 3572.0412 and times > 0
processNav(): length(Nav.depth) = 26916
processNav(): length(gindx)     = 26916
 
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/2003/2003317/2003.317.04/gps.nc')
Creating vector time with 72 elements.
Creating vector UTCTime with 72 elements.
Creating vector time with 72 elements.
Creating vector latitude with 72 elements.
Creating vector time with 72 elements.
Creating vector longitude with 72 elements.
Creating vector time with 72 elements.
Creating vector quality with 72 elements.
Creating vector time with 72 elements.
Creating vector numberOfSatellites with 72 elements.
Creating vector time with 72 elements.
Creating vector hdop with 72 elements.
Creating vector time with 72 elements.
Creating vector antennaHeight with 72 elements.
Creating vector time with 72 elements.
Creating vector geoHeight with 72 elements.
Creating vector time with 72 elements.
Creating vector dgpsDataAge with 72 elements.
Creating vector time with 72 elements.
Creating vector dgpsRSID with 72 elements.
Creating vector time with 72 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/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/2003/2003317/2003.317.04/parosci.nc')
Creating vector time with 26994 elements.
Creating vector depth with 26994 elements.
Creating vector time with 26994 elements.
Creating vector temp with 26994 elements.
Creating vector time with 26994 elements.
Creating vector pressure with 26994 elements.
Creating vector time with 26994 elements.
Creating vector temp_period with 26994 elements.
Creating vector time with 26994 elements.
Creating vector pres_period with 26994 elements.
Creating vector time with 26994 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.36052 max(Depth.data) = 1001.8545
Found 18718 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.36052 max(Depth.data) = 299.987
 
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/2003/2003317/2003.317.04/hydroscatlog.nc')
Creating vector time with 19213 elements.
Creating vector Seconds with 19213 elements.
Creating vector time with 19213 elements.
Creating vector HundrethsOfSeconds with 19213 elements.
Creating vector time with 19213 elements.
Creating vector Snorm1 with 19213 elements.
Creating vector time with 19213 elements.
Creating vector Snorm2 with 19213 elements.
Creating vector time with 19213 elements.
Creating vector Snorm3 with 19213 elements.
Creating vector time with 19213 elements.
Creating vector Gain_Status_1 with 19213 elements.
Creating vector time with 19213 elements.
Creating vector Gain_Status_2 with 19213 elements.
Creating vector time with 19213 elements.
Creating vector Gain_Status_3 with 19213 elements.
Creating vector time with 19213 elements.
Creating vector RawDepthValue with 19213 elements.
Creating vector time with 19213 elements.
Creating vector RawTempValue with 19213 elements.
Creating vector time with 19213 elements.
Creating vector Temperature with 19213 elements.
Creating vector time with 19213 elements.
Creating vector ErrorValue with 19213 elements.
Creating vector time with 19213 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/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/2003/2003317/2003.317.04/ctdDriver.nc')
Creating vector time with 21540 elements.
Creating vector conductivity with 21540 elements.
Creating vector time with 21540 elements.
Creating vector temperature with 21540 elements.
Creating vector time with 21540 elements.
Creating vector cond_frequency with 21540 elements.
Creating vector time with 21540 elements.
Creating vector temp_frequency with 21540 elements.
Creating vector time with 21540 elements.
Creating vector spare with 21540 elements.
Creating vector time with 21540 elements.
Creating vector humidity with 21540 elements.
Creating vector time with 21540 elements.
Creating vector flow1 with 21540 elements.
Creating vector time with 21540 elements.
Creating vector OBS with 21540 elements.
Creating vector time with 21540 elements.
Creating vector dissolvedO2 with 21540 elements.
Creating vector time with 21540 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/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/2003/2003317/2003.317.04/ctdDriver2.nc')
Creating vector time with 21539 elements.
Creating vector conductivity with 21539 elements.
Creating vector time with 21539 elements.
Creating vector temperature with 21539 elements.
Creating vector time with 21539 elements.
Creating vector cond_frequency with 21539 elements.
Creating vector time with 21539 elements.
Creating vector temp_frequency with 21539 elements.
Creating vector time with 21539 elements.
Creating vector flow2 with 21539 elements.
Creating vector time with 21539 elements.
Creating vector spare with 21539 elements.
Creating vector time with 21539 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/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/2003/2003317/2003.317.04/isuslog.nc')
Creating vector time with 3228 elements.
Creating vector isusNitrate with 3228 elements.
Creating vector time with 3228 elements.
Creating vector isusTemp with 3228 elements.
Creating vector time with 3228 elements.
Creating vector isusQuality with 3228 elements.
Creating vector time with 3228 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/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 75)
  In processBiolume (line 21)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
[Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 75)
  In processBiolume (line 22)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
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/2003/2003317/2003.317.04/lopc.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/lopc.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/lopc.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003317/2003.317.04/lopc.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


*** Setting lopc structure to NaNs. *** 
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.317.04.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_2003.317.02.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.317.03.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.317.04.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 2 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04.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 = 8 Gridding with nix = 24, iZ = 2001
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...
   bbp470
   bbp676
   fl676_uncorr
   N
   BL
Only one good point or fewer - NaNing the gBL array.
   BLflow
Only one good point or fewer - NaNing the gBLflow array.
   LOPC
Only one good point or fewer - NaNing the gLOPCcount array.
                             - NaNing the gLOPCtransCount array.
                             - NaNing the gLOPCnonTransCount array.
                             - NaNing the gLOPCLCcount array.
 
Masking and filtering with median filter of size 5...
  cvarname = gT
  cvarname = gS
  cvarname = gO
  cvarname = gN
  cvarname = gF
  cvarname = gB470
  cvarname = gB676
  cvarname = gBL
No valid data for gBL
  cvarname = gBLflow
No valid data for gBLflow
  cvarname = gLOPCcount
No valid data for gLOPCcount
  cvarname = gLOPCtransCount
No valid data for gLOPCtransCount
  cvarname = gLOPCnonTransCount
No valid data for gLOPCnonTransCount
  cvarname = gLOPCLCcount
No valid data for gLOPCLCcount
Encountered 0 NaN values in array of lon that is 20558 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 20558 points from grid Monterey25.grd (2876 x 2447)
Executing: /bin/rm -f ../results/2003317_GulperTimes.txt && touch ../results/2003317_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/2003/2003317/2003.317.02/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003317/2003.317.02/syslog -startEsecs 1068748733.1338 -surveyName Dorado389_2003_317_02_317_04 >> ../results/2003317_GulperTimes.txt
Executing: removeGulpDups.py ../results/2003317_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/2003/2003317/2003.317.03/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003317/2003.317.03/syslog -startEsecs 1068748733.1338 -surveyName Dorado389_2003_317_02_317_04 >> ../results/2003317_GulperTimes.txt
Executing: removeGulpDups.py ../results/2003317_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/2003/2003317/2003.317.04/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003317/2003.317.04/syslog -startEsecs 1068748733.1338 -surveyName Dorado389_2003_317_02_317_04 >> ../results/2003317_GulperTimes.txt
Executing: removeGulpDups.py ../results/2003317_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_gridded.mat

outvarstr =

    'gF gT gN gS gD gO gB470 gB676 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
2Column contouring gridded variable gT
2Column contouring gridded variable gS
2Column contouring gridded variable gN
2Column contouring gridded variable gO
2Column contouring gridded variable gB470
2Column contouring gridded variable gB676
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_2column.png
Elapsed time to save image: 4 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 gB470
Biolume contouring gridded variable gB676
Biolume contouring gridded variable gF
Biolume contouring gridded variable gBL
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_biolume.png
Elapsed time to save image: 21 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 gB470
2Column contouring gridded variable gB676
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_lopc.png
Elapsed time to save image: 4 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_2003_317_02_317_04_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_2column.png...
Copied to /mbari/AUVCTD/surveys/2003/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_biolume.png...
Copied to /mbari/AUVCTD/surveys/2003/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_lopc.png...
Copied to /mbari/AUVCTD/surveys/2003/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2003/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2003/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2003/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing KML files ...
KML = write_kml(survey_shrt_filename_base, 'Temperature', jetplus, varlimits(1,:), ctd1.T, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Temperature.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2003/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Salinity.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2003/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2003/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Oxygen.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2003/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @470 nm', jetplus, varlimits(5,:), hs2.bbp470, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Optical_Backscatter_470_nm.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Optical_Backscatter_470_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2003/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Optical_Backscatter_676_nm.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Optical_Backscatter_676_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2003/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Chlorophyll_Fluorescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2003/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2003/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2003/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2003_317_02_317_04.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04.kml...
Copied to /mbari/AUVCTD/surveys/2003/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_317_02_317_04_LOPC_Total_Count.kml'
not found.] 
[> In create_data_products (line 414)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
Encountered 3238 NaN values in array of lon that is 5659 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 2421 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 2421 are not equal to number of Lat lon points = 5659
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_2003_317_02_317_04.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04.txt...
Copied to /mbari/AUVCTD/surveys/2003/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_Gulper.txt...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2003/odv/
cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_decim.nc...
Copied to /mbari/AUVCTD/surveys/2003/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_2003_317_02_317_04.nc...
Copied to /mbari/AUVCTD/surveys/2003/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2003/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_317_02_317_04.mat...
Copied to /mbari/AUVCTD/surveys/2003/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2003_317_02_317_04 processed" mccann@mbari.org < mail_Dorado389_2003_317_02_317_04.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.317.02.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.317.03.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.317.04.mat
Processing time: 48 seconds