Execution of AUVprocess_main version 1.86 at 2018-06-02T01:37:57Z on elvis
Matlab command executed: 
   AUVprocess_main('OCCO', 2003, ['233.02';'233.03';'233.04';'233.05';'233.06'], '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: 2003.233.02
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.02/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.02/
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/2003/2003233/2003.233.02/navigation.nc')
Creating vector time with 18556 elements.
Creating vector mPos_x with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mPos_y with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mDepth with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mGpsNorth with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mGpsEast with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mGpsValid with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mPhi with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mTheta with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mPsi with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mOmega_x with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mOmega_y with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mOmega_z with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mPsaRange with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mAltitude with 18556 elements.
Creating vector time with 18556 elements.
Creating vector mWaterSpeed with 18556 elements.
Creating vector time with 18556 elements.
Creating vector nfix with 18556 elements.
Creating vector time with 18556 elements.
Creating vector efix with 18556 elements.
Creating vector time with 18556 elements.
Creating vector filter_north with 18556 elements.
Creating vector time with 18556 elements.
Creating vector filter_east with 18556 elements.
Creating vector time with 18556 elements.
Creating vector filter_depth with 18556 elements.
Creating vector time with 18556 elements.
Creating vector north_current with 18556 elements.
Creating vector time with 18556 elements.
Creating vector east_current with 18556 elements.
Creating vector time with 18556 elements.
Creating vector speed_bias with 18556 elements.
Creating vector time with 18556 elements.
Creating vector heading_bias with 18556 elements.
Creating vector time with 18556 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.02/navigation.nc');
processNav(): median of positive valued depths = 10.1536
processNav(): Finding depths less than 71.0754 and times > 0
processNav(): length(Nav.depth) = 18556
processNav(): length(gindx)     = 18556
 
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/2003/2003233/2003.233.02/gps.nc')
Creating vector time with 281 elements.
Creating vector UTCTime with 281 elements.
Creating vector time with 281 elements.
Creating vector latitude with 281 elements.
Creating vector time with 281 elements.
Creating vector longitude with 281 elements.
Creating vector time with 281 elements.
Creating vector quality with 281 elements.
Creating vector time with 281 elements.
Creating vector numberOfSatellites with 281 elements.
Creating vector time with 281 elements.
Creating vector hdop with 281 elements.
Creating vector time with 281 elements.
Creating vector antennaHeight with 281 elements.
Creating vector time with 281 elements.
Creating vector geoHeight with 281 elements.
Creating vector time with 281 elements.
Creating vector dgpsDataAge with 281 elements.
Creating vector time with 281 elements.
Creating vector dgpsRSID with 281 elements.
Creating vector time with 281 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/parosci.nc')
Creating vector time with 18659 elements.
Creating vector depth with 18659 elements.
Creating vector time with 18659 elements.
Creating vector temp with 18659 elements.
Creating vector time with 18659 elements.
Creating vector pressure with 18659 elements.
Creating vector time with 18659 elements.
Creating vector temp_period with 18659 elements.
Creating vector time with 18659 elements.
Creating vector pres_period with 18659 elements.
Creating vector time with 18659 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.02/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.17335 max(Depth.data) = 49.0649
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.17335 max(Depth.data) = 49.0649
 
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/2003/2003233/2003.233.02/hydroscatlog.nc')
Creating vector time with 14906 elements.
Creating vector Seconds with 14906 elements.
Creating vector time with 14906 elements.
Creating vector HundrethsOfSeconds with 14906 elements.
Creating vector time with 14906 elements.
Creating vector Snorm1 with 14906 elements.
Creating vector time with 14906 elements.
Creating vector Snorm2 with 14906 elements.
Creating vector time with 14906 elements.
Creating vector Snorm3 with 14906 elements.
Creating vector time with 14906 elements.
Creating vector Gain_Status_1 with 14906 elements.
Creating vector time with 14906 elements.
Creating vector Gain_Status_2 with 14906 elements.
Creating vector time with 14906 elements.
Creating vector Gain_Status_3 with 14906 elements.
Creating vector time with 14906 elements.
Creating vector RawDepthValue with 14906 elements.
Creating vector time with 14906 elements.
Creating vector RawTempValue with 14906 elements.
Creating vector time with 14906 elements.
Creating vector Temperature with 14906 elements.
Creating vector time with 14906 elements.
Creating vector ErrorValue with 14906 elements.
Creating vector time with 14906 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/ctdDriver.nc')
Creating vector time with 14851 elements.
Creating vector conductivity with 14851 elements.
Creating vector time with 14851 elements.
Creating vector temperature with 14851 elements.
Creating vector time with 14851 elements.
Creating vector cond_frequency with 14851 elements.
Creating vector time with 14851 elements.
Creating vector temp_frequency with 14851 elements.
Creating vector time with 14851 elements.
Creating vector spare with 14851 elements.
Creating vector time with 14851 elements.
Creating vector humidity with 14851 elements.
Creating vector time with 14851 elements.
Creating vector flow1 with 14851 elements.
Creating vector time with 14851 elements.
Creating vector OBS with 14851 elements.
Creating vector time with 14851 elements.
Creating vector dissolvedO2 with 14851 elements.
Creating vector time with 14851 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.02/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/ctdDriver2.nc')
Creating vector time with 14850 elements.
Creating vector conductivity with 14850 elements.
Creating vector time with 14850 elements.
Creating vector temperature with 14850 elements.
Creating vector time with 14850 elements.
Creating vector cond_frequency with 14850 elements.
Creating vector time with 14850 elements.
Creating vector temp_frequency with 14850 elements.
Creating vector time with 14850 elements.
Creating vector flow2 with 14850 elements.
Creating vector time with 14850 elements.
Creating vector spare with 14850 elements.
Creating vector time with 14850 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.02/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/isuslog.nc')
Creating vector time with 2211 elements.
Creating vector isusNitrate with 2211 elements.
Creating vector time with 2211 elements.
Creating vector isusTemp with 2211 elements.
Creating vector time with 2211 elements.
Creating vector isusQuality with 2211 elements.
Creating vector time with 2211 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/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/2003/2003233/2003.233.02/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_2003.233.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
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*************************************************************************
Processing AUV mission: 2003.233.03
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.03/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.03/
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/2003/2003233/2003.233.03/navigation.nc')
Creating vector time with 26025 elements.
Creating vector mPos_x with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mPos_y with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mDepth with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mGpsNorth with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mGpsEast with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mGpsValid with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mPhi with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mTheta with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mPsi with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mOmega_x with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mOmega_y with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mOmega_z with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mPsaRange with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mAltitude with 26025 elements.
Creating vector time with 26025 elements.
Creating vector mWaterSpeed with 26025 elements.
Creating vector time with 26025 elements.
Creating vector nfix with 26025 elements.
Creating vector time with 26025 elements.
Creating vector efix with 26025 elements.
Creating vector time with 26025 elements.
Creating vector filter_north with 26025 elements.
Creating vector time with 26025 elements.
Creating vector filter_east with 26025 elements.
Creating vector time with 26025 elements.
Creating vector filter_depth with 26025 elements.
Creating vector time with 26025 elements.
Creating vector north_current with 26025 elements.
Creating vector time with 26025 elements.
Creating vector east_current with 26025 elements.
Creating vector time with 26025 elements.
Creating vector speed_bias with 26025 elements.
Creating vector time with 26025 elements.
Creating vector heading_bias with 26025 elements.
Creating vector time with 26025 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.03/navigation.nc');
processNav(): median of positive valued depths = 21.9838
processNav(): Finding depths less than 153.8868 and times > 0
processNav(): length(Nav.depth) = 26025
processNav(): length(gindx)     = 26025
 
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/2003/2003233/2003.233.03/gps.nc')
Creating vector time with 277 elements.
Creating vector UTCTime with 277 elements.
Creating vector time with 277 elements.
Creating vector latitude with 277 elements.
Creating vector time with 277 elements.
Creating vector longitude with 277 elements.
Creating vector time with 277 elements.
Creating vector quality with 277 elements.
Creating vector time with 277 elements.
Creating vector numberOfSatellites with 277 elements.
Creating vector time with 277 elements.
Creating vector hdop with 277 elements.
Creating vector time with 277 elements.
Creating vector antennaHeight with 277 elements.
Creating vector time with 277 elements.
Creating vector geoHeight with 277 elements.
Creating vector time with 277 elements.
Creating vector dgpsDataAge with 277 elements.
Creating vector time with 277 elements.
Creating vector dgpsRSID with 277 elements.
Creating vector time with 277 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/parosci.nc')
Creating vector time with 26131 elements.
Creating vector depth with 26131 elements.
Creating vector time with 26131 elements.
Creating vector temp with 26131 elements.
Creating vector time with 26131 elements.
Creating vector pressure with 26131 elements.
Creating vector time with 26131 elements.
Creating vector temp_period with 26131 elements.
Creating vector time with 26131 elements.
Creating vector pres_period with 26131 elements.
Creating vector time with 26131 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.03/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.082561 max(Depth.data) = 52.0093
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.082561 max(Depth.data) = 52.0093
 
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/2003/2003233/2003.233.03/hydroscatlog.nc')
Creating vector time with 20880 elements.
Creating vector Seconds with 20880 elements.
Creating vector time with 20880 elements.
Creating vector HundrethsOfSeconds with 20880 elements.
Creating vector time with 20880 elements.
Creating vector Snorm1 with 20880 elements.
Creating vector time with 20880 elements.
Creating vector Snorm2 with 20880 elements.
Creating vector time with 20880 elements.
Creating vector Snorm3 with 20880 elements.
Creating vector time with 20880 elements.
Creating vector Gain_Status_1 with 20880 elements.
Creating vector time with 20880 elements.
Creating vector Gain_Status_2 with 20880 elements.
Creating vector time with 20880 elements.
Creating vector Gain_Status_3 with 20880 elements.
Creating vector time with 20880 elements.
Creating vector RawDepthValue with 20880 elements.
Creating vector time with 20880 elements.
Creating vector RawTempValue with 20880 elements.
Creating vector time with 20880 elements.
Creating vector Temperature with 20880 elements.
Creating vector time with 20880 elements.
Creating vector ErrorValue with 20880 elements.
Creating vector time with 20880 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/ctdDriver.nc')
Creating vector time with 20826 elements.
Creating vector conductivity with 20826 elements.
Creating vector time with 20826 elements.
Creating vector temperature with 20826 elements.
Creating vector time with 20826 elements.
Creating vector cond_frequency with 20826 elements.
Creating vector time with 20826 elements.
Creating vector temp_frequency with 20826 elements.
Creating vector time with 20826 elements.
Creating vector spare with 20826 elements.
Creating vector time with 20826 elements.
Creating vector humidity with 20826 elements.
Creating vector time with 20826 elements.
Creating vector flow1 with 20826 elements.
Creating vector time with 20826 elements.
Creating vector OBS with 20826 elements.
Creating vector time with 20826 elements.
Creating vector dissolvedO2 with 20826 elements.
Creating vector time with 20826 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.03/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/ctdDriver2.nc')
Creating vector time with 20826 elements.
Creating vector conductivity with 20826 elements.
Creating vector time with 20826 elements.
Creating vector temperature with 20826 elements.
Creating vector time with 20826 elements.
Creating vector cond_frequency with 20826 elements.
Creating vector time with 20826 elements.
Creating vector temp_frequency with 20826 elements.
Creating vector time with 20826 elements.
Creating vector flow2 with 20826 elements.
Creating vector time with 20826 elements.
Creating vector spare with 20826 elements.
Creating vector time with 20826 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.03/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/isuslog.nc')
Creating vector time with 3111 elements.
Creating vector isusNitrate with 3111 elements.
Creating vector time with 3111 elements.
Creating vector isusTemp with 3111 elements.
Creating vector time with 3111 elements.
Creating vector isusQuality with 3111 elements.
Creating vector time with 3111 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/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/2003/2003233/2003.233.03/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_2003.233.03.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2003.233.04
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.04/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.04/
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/2003/2003233/2003.233.04/navigation.nc')
Creating vector time with 19501 elements.
Creating vector mPos_x with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mPos_y with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mDepth with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mGpsNorth with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mGpsEast with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mGpsValid with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mPhi with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mTheta with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mPsi with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mOmega_x with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mOmega_y with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mOmega_z with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mPsaRange with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mAltitude with 19501 elements.
Creating vector time with 19501 elements.
Creating vector mWaterSpeed with 19501 elements.
Creating vector time with 19501 elements.
Creating vector nfix with 19501 elements.
Creating vector time with 19501 elements.
Creating vector efix with 19501 elements.
Creating vector time with 19501 elements.
Creating vector filter_north with 19501 elements.
Creating vector time with 19501 elements.
Creating vector filter_east with 19501 elements.
Creating vector time with 19501 elements.
Creating vector filter_depth with 19501 elements.
Creating vector time with 19501 elements.
Creating vector north_current with 19501 elements.
Creating vector time with 19501 elements.
Creating vector east_current with 19501 elements.
Creating vector time with 19501 elements.
Creating vector speed_bias with 19501 elements.
Creating vector time with 19501 elements.
Creating vector heading_bias with 19501 elements.
Creating vector time with 19501 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.04/navigation.nc');
processNav(): median of positive valued depths = 27.1417
processNav(): Finding depths less than 189.9919 and times > 0
processNav(): length(Nav.depth) = 19501
processNav(): length(gindx)     = 19501
 
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/2003/2003233/2003.233.04/gps.nc')
Creating vector time with 266 elements.
Creating vector UTCTime with 266 elements.
Creating vector time with 266 elements.
Creating vector latitude with 266 elements.
Creating vector time with 266 elements.
Creating vector longitude with 266 elements.
Creating vector time with 266 elements.
Creating vector quality with 266 elements.
Creating vector time with 266 elements.
Creating vector numberOfSatellites with 266 elements.
Creating vector time with 266 elements.
Creating vector hdop with 266 elements.
Creating vector time with 266 elements.
Creating vector antennaHeight with 266 elements.
Creating vector time with 266 elements.
Creating vector geoHeight with 266 elements.
Creating vector time with 266 elements.
Creating vector dgpsDataAge with 266 elements.
Creating vector time with 266 elements.
Creating vector dgpsRSID with 266 elements.
Creating vector time with 266 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/parosci.nc')
Creating vector time with 19605 elements.
Creating vector depth with 19605 elements.
Creating vector time with 19605 elements.
Creating vector temp with 19605 elements.
Creating vector time with 19605 elements.
Creating vector pressure with 19605 elements.
Creating vector time with 19605 elements.
Creating vector temp_period with 19605 elements.
Creating vector time with 19605 elements.
Creating vector pres_period with 19605 elements.
Creating vector time with 19605 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.04/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.10929 max(Depth.data) = 62.4492
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.10929 max(Depth.data) = 62.4492
 
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/2003/2003233/2003.233.04/hydroscatlog.nc')
Creating vector time with 15663 elements.
Creating vector Seconds with 15663 elements.
Creating vector time with 15663 elements.
Creating vector HundrethsOfSeconds with 15663 elements.
Creating vector time with 15663 elements.
Creating vector Snorm1 with 15663 elements.
Creating vector time with 15663 elements.
Creating vector Snorm2 with 15663 elements.
Creating vector time with 15663 elements.
Creating vector Snorm3 with 15663 elements.
Creating vector time with 15663 elements.
Creating vector Gain_Status_1 with 15663 elements.
Creating vector time with 15663 elements.
Creating vector Gain_Status_2 with 15663 elements.
Creating vector time with 15663 elements.
Creating vector Gain_Status_3 with 15663 elements.
Creating vector time with 15663 elements.
Creating vector RawDepthValue with 15663 elements.
Creating vector time with 15663 elements.
Creating vector RawTempValue with 15663 elements.
Creating vector time with 15663 elements.
Creating vector Temperature with 15663 elements.
Creating vector time with 15663 elements.
Creating vector ErrorValue with 15663 elements.
Creating vector time with 15663 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/ctdDriver.nc')
Creating vector time with 15604 elements.
Creating vector conductivity with 15604 elements.
Creating vector time with 15604 elements.
Creating vector temperature with 15604 elements.
Creating vector time with 15604 elements.
Creating vector cond_frequency with 15604 elements.
Creating vector time with 15604 elements.
Creating vector temp_frequency with 15604 elements.
Creating vector time with 15604 elements.
Creating vector spare with 15604 elements.
Creating vector time with 15604 elements.
Creating vector humidity with 15604 elements.
Creating vector time with 15604 elements.
Creating vector flow1 with 15604 elements.
Creating vector time with 15604 elements.
Creating vector OBS with 15604 elements.
Creating vector time with 15604 elements.
Creating vector dissolvedO2 with 15604 elements.
Creating vector time with 15604 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.04/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/ctdDriver2.nc')
Creating vector time with 15603 elements.
Creating vector conductivity with 15603 elements.
Creating vector time with 15603 elements.
Creating vector temperature with 15603 elements.
Creating vector time with 15603 elements.
Creating vector cond_frequency with 15603 elements.
Creating vector time with 15603 elements.
Creating vector temp_frequency with 15603 elements.
Creating vector time with 15603 elements.
Creating vector flow2 with 15603 elements.
Creating vector time with 15603 elements.
Creating vector spare with 15603 elements.
Creating vector time with 15603 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.04/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/isuslog.nc')
Creating vector time with 2325 elements.
Creating vector isusNitrate with 2325 elements.
Creating vector time with 2325 elements.
Creating vector isusTemp with 2325 elements.
Creating vector time with 2325 elements.
Creating vector isusQuality with 2325 elements.
Creating vector time with 2325 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/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/2003/2003233/2003.233.04/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_2003.233.04.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2003.233.05
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.05/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.05/
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/2003/2003233/2003.233.05/navigation.nc')
Creating vector time with 22609 elements.
Creating vector mPos_x with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mPos_y with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mDepth with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mGpsNorth with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mGpsEast with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mGpsValid with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mPhi with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mTheta with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mPsi with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mOmega_x with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mOmega_y with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mOmega_z with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mPsaRange with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mAltitude with 22609 elements.
Creating vector time with 22609 elements.
Creating vector mWaterSpeed with 22609 elements.
Creating vector time with 22609 elements.
Creating vector nfix with 22609 elements.
Creating vector time with 22609 elements.
Creating vector efix with 22609 elements.
Creating vector time with 22609 elements.
Creating vector filter_north with 22609 elements.
Creating vector time with 22609 elements.
Creating vector filter_east with 22609 elements.
Creating vector time with 22609 elements.
Creating vector filter_depth with 22609 elements.
Creating vector time with 22609 elements.
Creating vector north_current with 22609 elements.
Creating vector time with 22609 elements.
Creating vector east_current with 22609 elements.
Creating vector time with 22609 elements.
Creating vector speed_bias with 22609 elements.
Creating vector time with 22609 elements.
Creating vector heading_bias with 22609 elements.
Creating vector time with 22609 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.05/navigation.nc');
processNav(): median of positive valued depths = 32.2723
processNav(): Finding depths less than 225.9063 and times > 0
processNav(): length(Nav.depth) = 22609
processNav(): length(gindx)     = 22609
 
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/2003/2003233/2003.233.05/gps.nc')
Creating vector time with 289 elements.
Creating vector UTCTime with 289 elements.
Creating vector time with 289 elements.
Creating vector latitude with 289 elements.
Creating vector time with 289 elements.
Creating vector longitude with 289 elements.
Creating vector time with 289 elements.
Creating vector quality with 289 elements.
Creating vector time with 289 elements.
Creating vector numberOfSatellites with 289 elements.
Creating vector time with 289 elements.
Creating vector hdop with 289 elements.
Creating vector time with 289 elements.
Creating vector antennaHeight with 289 elements.
Creating vector time with 289 elements.
Creating vector geoHeight with 289 elements.
Creating vector time with 289 elements.
Creating vector dgpsDataAge with 289 elements.
Creating vector time with 289 elements.
Creating vector dgpsRSID with 289 elements.
Creating vector time with 289 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/parosci.nc')
Creating vector time with 22713 elements.
Creating vector depth with 22713 elements.
Creating vector time with 22713 elements.
Creating vector temp with 22713 elements.
Creating vector time with 22713 elements.
Creating vector pressure with 22713 elements.
Creating vector time with 22713 elements.
Creating vector temp_period with 22713 elements.
Creating vector time with 22713 elements.
Creating vector pres_period with 22713 elements.
Creating vector time with 22713 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.05/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.1162 max(Depth.data) = 64.5788
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.1162 max(Depth.data) = 64.5788
 
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/2003/2003233/2003.233.05/hydroscatlog.nc')
Creating vector time with 18147 elements.
Creating vector Seconds with 18147 elements.
Creating vector time with 18147 elements.
Creating vector HundrethsOfSeconds with 18147 elements.
Creating vector time with 18147 elements.
Creating vector Snorm1 with 18147 elements.
Creating vector time with 18147 elements.
Creating vector Snorm2 with 18147 elements.
Creating vector time with 18147 elements.
Creating vector Snorm3 with 18147 elements.
Creating vector time with 18147 elements.
Creating vector Gain_Status_1 with 18147 elements.
Creating vector time with 18147 elements.
Creating vector Gain_Status_2 with 18147 elements.
Creating vector time with 18147 elements.
Creating vector Gain_Status_3 with 18147 elements.
Creating vector time with 18147 elements.
Creating vector RawDepthValue with 18147 elements.
Creating vector time with 18147 elements.
Creating vector RawTempValue with 18147 elements.
Creating vector time with 18147 elements.
Creating vector Temperature with 18147 elements.
Creating vector time with 18147 elements.
Creating vector ErrorValue with 18147 elements.
Creating vector time with 18147 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/ctdDriver.nc')
Creating vector time with 18092 elements.
Creating vector conductivity with 18092 elements.
Creating vector time with 18092 elements.
Creating vector temperature with 18092 elements.
Creating vector time with 18092 elements.
Creating vector cond_frequency with 18092 elements.
Creating vector time with 18092 elements.
Creating vector temp_frequency with 18092 elements.
Creating vector time with 18092 elements.
Creating vector spare with 18092 elements.
Creating vector time with 18092 elements.
Creating vector humidity with 18092 elements.
Creating vector time with 18092 elements.
Creating vector flow1 with 18092 elements.
Creating vector time with 18092 elements.
Creating vector OBS with 18092 elements.
Creating vector time with 18092 elements.
Creating vector dissolvedO2 with 18092 elements.
Creating vector time with 18092 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.05/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/ctdDriver2.nc')
Creating vector time with 18091 elements.
Creating vector conductivity with 18091 elements.
Creating vector time with 18091 elements.
Creating vector temperature with 18091 elements.
Creating vector time with 18091 elements.
Creating vector cond_frequency with 18091 elements.
Creating vector time with 18091 elements.
Creating vector temp_frequency with 18091 elements.
Creating vector time with 18091 elements.
Creating vector flow2 with 18091 elements.
Creating vector time with 18091 elements.
Creating vector spare with 18091 elements.
Creating vector time with 18091 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.05/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/isuslog.nc')
Creating vector time with 2702 elements.
Creating vector isusNitrate with 2702 elements.
Creating vector time with 2702 elements.
Creating vector isusTemp with 2702 elements.
Creating vector time with 2702 elements.
Creating vector isusQuality with 2702 elements.
Creating vector time with 2702 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/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/2003/2003233/2003.233.05/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_2003.233.05.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2003.233.06
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.06/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.06/
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/2003/2003233/2003.233.06/navigation.nc')
Creating vector time with 22410 elements.
Creating vector mPos_x with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mPos_y with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mDepth with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mGpsNorth with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mGpsEast with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mGpsValid with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mPhi with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mTheta with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mPsi with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mOmega_x with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mOmega_y with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mOmega_z with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mPsaRange with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mAltitude with 22410 elements.
Creating vector time with 22410 elements.
Creating vector mWaterSpeed with 22410 elements.
Creating vector time with 22410 elements.
Creating vector nfix with 22410 elements.
Creating vector time with 22410 elements.
Creating vector efix with 22410 elements.
Creating vector time with 22410 elements.
Creating vector filter_north with 22410 elements.
Creating vector time with 22410 elements.
Creating vector filter_east with 22410 elements.
Creating vector time with 22410 elements.
Creating vector filter_depth with 22410 elements.
Creating vector time with 22410 elements.
Creating vector north_current with 22410 elements.
Creating vector time with 22410 elements.
Creating vector east_current with 22410 elements.
Creating vector time with 22410 elements.
Creating vector speed_bias with 22410 elements.
Creating vector time with 22410 elements.
Creating vector heading_bias with 22410 elements.
Creating vector time with 22410 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.06/navigation.nc');
processNav(): median of positive valued depths = 32.3875
processNav(): Finding depths less than 226.7128 and times > 0
processNav(): length(Nav.depth) = 22410
processNav(): length(gindx)     = 22410
 
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/2003/2003233/2003.233.06/gps.nc')
Creating vector time with 270 elements.
Creating vector UTCTime with 270 elements.
Creating vector time with 270 elements.
Creating vector latitude with 270 elements.
Creating vector time with 270 elements.
Creating vector longitude with 270 elements.
Creating vector time with 270 elements.
Creating vector quality with 270 elements.
Creating vector time with 270 elements.
Creating vector numberOfSatellites with 270 elements.
Creating vector time with 270 elements.
Creating vector hdop with 270 elements.
Creating vector time with 270 elements.
Creating vector antennaHeight with 270 elements.
Creating vector time with 270 elements.
Creating vector geoHeight with 270 elements.
Creating vector time with 270 elements.
Creating vector dgpsDataAge with 270 elements.
Creating vector time with 270 elements.
Creating vector dgpsRSID with 270 elements.
Creating vector time with 270 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/parosci.nc')
Creating vector time with 22514 elements.
Creating vector depth with 22514 elements.
Creating vector time with 22514 elements.
Creating vector temp with 22514 elements.
Creating vector time with 22514 elements.
Creating vector pressure with 22514 elements.
Creating vector time with 22514 elements.
Creating vector temp_period with 22514 elements.
Creating vector time with 22514 elements.
Creating vector pres_period with 22514 elements.
Creating vector time with 22514 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.06/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.089281 max(Depth.data) = 70.9993
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.089281 max(Depth.data) = 70.9993
 
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/2003/2003233/2003.233.06/hydroscatlog.nc')
Creating vector time with 17989 elements.
Creating vector Seconds with 17989 elements.
Creating vector time with 17989 elements.
Creating vector HundrethsOfSeconds with 17989 elements.
Creating vector time with 17989 elements.
Creating vector Snorm1 with 17989 elements.
Creating vector time with 17989 elements.
Creating vector Snorm2 with 17989 elements.
Creating vector time with 17989 elements.
Creating vector Snorm3 with 17989 elements.
Creating vector time with 17989 elements.
Creating vector Gain_Status_1 with 17989 elements.
Creating vector time with 17989 elements.
Creating vector Gain_Status_2 with 17989 elements.
Creating vector time with 17989 elements.
Creating vector Gain_Status_3 with 17989 elements.
Creating vector time with 17989 elements.
Creating vector RawDepthValue with 17989 elements.
Creating vector time with 17989 elements.
Creating vector RawTempValue with 17989 elements.
Creating vector time with 17989 elements.
Creating vector Temperature with 17989 elements.
Creating vector time with 17989 elements.
Creating vector ErrorValue with 17989 elements.
Creating vector time with 17989 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/ctdDriver.nc')
Creating vector time with 17934 elements.
Creating vector conductivity with 17934 elements.
Creating vector time with 17934 elements.
Creating vector temperature with 17934 elements.
Creating vector time with 17934 elements.
Creating vector cond_frequency with 17934 elements.
Creating vector time with 17934 elements.
Creating vector temp_frequency with 17934 elements.
Creating vector time with 17934 elements.
Creating vector spare with 17934 elements.
Creating vector time with 17934 elements.
Creating vector humidity with 17934 elements.
Creating vector time with 17934 elements.
Creating vector flow1 with 17934 elements.
Creating vector time with 17934 elements.
Creating vector OBS with 17934 elements.
Creating vector time with 17934 elements.
Creating vector dissolvedO2 with 17934 elements.
Creating vector time with 17934 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.06/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/ctdDriver2.nc')
Creating vector time with 17933 elements.
Creating vector conductivity with 17933 elements.
Creating vector time with 17933 elements.
Creating vector temperature with 17933 elements.
Creating vector time with 17933 elements.
Creating vector cond_frequency with 17933 elements.
Creating vector time with 17933 elements.
Creating vector temp_frequency with 17933 elements.
Creating vector time with 17933 elements.
Creating vector flow2 with 17933 elements.
Creating vector time with 17933 elements.
Creating vector spare with 17933 elements.
Creating vector time with 17933 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.06/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/isuslog.nc')
Creating vector time with 2678 elements.
Creating vector isusNitrate with 2678 elements.
Creating vector time with 2678 elements.
Creating vector isusTemp with 2678 elements.
Creating vector time with 2678 elements.
Creating vector isusQuality with 2678 elements.
Creating vector time with 2678 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/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/2003/2003233/2003.233.06/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_2003.233.06.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_2003.233.02.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.233.03.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.233.04.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.233.05.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.233.06.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 10 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06.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 = 116 Gridding with nix = 348, iZ = 139
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 108983 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 108983 points from grid Monterey25.grd (2876 x 2447)
Executing: /bin/rm -f ../results/2003233_GulperTimes.txt && touch ../results/2003233_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/2003/2003233/2003.233.02/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003233/2003.233.02/syslog -startEsecs 1061500266.69 -surveyName Dorado389_2003_233_02_233_06 >> ../results/2003233_GulperTimes.txt
Executing: removeGulpDups.py ../results/2003233_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/2003/2003233/2003.233.03/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003233/2003.233.03/syslog -startEsecs 1061500266.69 -surveyName Dorado389_2003_233_02_233_06 >> ../results/2003233_GulperTimes.txt
Executing: removeGulpDups.py ../results/2003233_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/2003/2003233/2003.233.04/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003233/2003.233.04/syslog -startEsecs 1061500266.69 -surveyName Dorado389_2003_233_02_233_06 >> ../results/2003233_GulperTimes.txt
Executing: removeGulpDups.py ../results/2003233_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/2003/2003233/2003.233.05/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003233/2003.233.05/syslog -startEsecs 1061500266.69 -surveyName Dorado389_2003_233_02_233_06 >> ../results/2003233_GulperTimes.txt
Executing: removeGulpDups.py ../results/2003233_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/2003/2003233/2003.233.06/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003233/2003.233.06/syslog -startEsecs 1061500266.69 -surveyName Dorado389_2003_233_02_233_06 >> ../results/2003233_GulperTimes.txt
Executing: removeGulpDups.py ../results/2003233_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06_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
  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 gB470
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB676
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gF
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06_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 gB470
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gB676
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gF
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06_biolume.png
Elapsed time to save image: 31 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 gB470
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB676
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gF
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06_lopc.png
Elapsed time to save image: 9 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_233_02_233_06_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06_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_233_02_233_06_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_233_02_233_06_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_233_02_233_06_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_233_02_233_06_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_233_02_233_06_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_233_02_233_06_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_233_02_233_06_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_233_02_233_06_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_233_02_233_06_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_233_02_233_06_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_233_02_233_06_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_233_02_233_06_Oxygen.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_233_02_233_06_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_233_02_233_06_Optical_Backscatter_470_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_233_02_233_06_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_233_02_233_06_Optical_Backscatter_676_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_233_02_233_06_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_233_02_233_06_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_233_02_233_06_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_233_02_233_06_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_233_02_233_06_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_233_02_233_06_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_233_02_233_06_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_233_02_233_06.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06.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_233_02_233_06_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_233_02_233_06.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
4 NaNs found in bbpRed.  Interpolating anyway.
2 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 13 NaN values in array of lon that is 13027 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 13014 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 13014 are not equal to number of Lat lon points = 13027
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_233_02_233_06.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06.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_233_02_233_06_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_233_02_233_06_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
4 NaNs found in bbpRed.  Interpolating anyway.
2 NaNs found in flRed_uncorr.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_233_02_233_06_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_233_02_233_06.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_233_02_233_06_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_233_02_233_06.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_233_02_233_06 processed" mccann@mbari.org < mail_Dorado389_2003_233_02_233_06.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.233.02.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.233.03.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.233.04.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.233.05.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.233.06.mat
Processing time: 235 seconds