Execution of AUVprocess_main version 1.86 at 2018-05-30T22:54:48Z on elvis
Matlab command executed: 
   AUVprocess_main('OCCO', 2005, ['021.00';'021.01';'021.02';'021.03';'021.04'], '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: 2005.021.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/
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/2005/2005021/2005.021.00/navigation.nc')
Creating vector time with 41797 elements.
Creating vector mPos_x with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mPos_y with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mDepth with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mGpsNorth with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mGpsEast with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mGpsValid with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mPhi with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mTheta with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mPsi with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mOmega_x with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mOmega_y with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mOmega_z with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mPsaRange with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mAltitude with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mDvlAltitude with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mWaterSpeed with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mDvlValid with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mDvlNewData with 41797 elements.
Creating vector time with 41797 elements.
Creating vector mDeltaT with 41797 elements.
Creating vector time with 41797 elements.
Creating vector nfix with 41797 elements.
Creating vector time with 41797 elements.
Creating vector efix with 41797 elements.
Creating vector time with 41797 elements.
Creating vector filter_north with 41797 elements.
Creating vector time with 41797 elements.
Creating vector filter_east with 41797 elements.
Creating vector time with 41797 elements.
Creating vector filter_depth with 41797 elements.
Creating vector time with 41797 elements.
Creating vector north_current with 41797 elements.
Creating vector time with 41797 elements.
Creating vector east_current with 41797 elements.
Creating vector time with 41797 elements.
Creating vector speed_bias with 41797 elements.
Creating vector time with 41797 elements.
Creating vector heading_bias with 41797 elements.
Creating vector time with 41797 elements.
Creating vector latitude with 41797 elements.
Creating vector time with 41797 elements.
Creating vector longitude with 41797 elements.
Creating vector time with 41797 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/navigation.nc');
processNav(): median of positive valued depths = 7.4053
processNav(): Finding depths less than 51.8368 and times > 0
processNav(): length(Nav.depth) = 41797
processNav(): length(gindx)     = 41797
 
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/2005/2005021/2005.021.00/gps.nc')
Creating vector time with 486 elements.
Creating vector hours with 486 elements.
Creating vector time with 486 elements.
Creating vector minutes with 486 elements.
Creating vector time with 486 elements.
Creating vector seconds with 486 elements.
Creating vector time with 486 elements.
Creating vector centiSeconds with 486 elements.
Creating vector time with 486 elements.
Creating vector latitude with 486 elements.
Creating vector time with 486 elements.
Creating vector longitude with 486 elements.
Creating vector time with 486 elements.
Creating vector quality with 486 elements.
Creating vector time with 486 elements.
Creating vector numberOfSatellites with 486 elements.
Creating vector time with 486 elements.
Creating vector hdop with 486 elements.
Creating vector time with 486 elements.
Creating vector antennaHeight with 486 elements.
Creating vector time with 486 elements.
Creating vector geoHeight with 486 elements.
Creating vector time with 486 elements.
Creating vector dgpsDataAge with 486 elements.
Creating vector time with 486 elements.
Creating vector dgpsRSID with 486 elements.
Creating vector time with 486 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/gps.nc');
 
Processing depth data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/parosci.nc')
Creating vector time with 41226 elements.
Creating vector depth with 41226 elements.
Creating vector time with 41226 elements.
Creating vector temp with 41226 elements.
Creating vector time with 41226 elements.
Creating vector pressure with 41226 elements.
Creating vector time with 41226 elements.
Creating vector temp_period with 41226 elements.
Creating vector time with 41226 elements.
Creating vector pres_period with 41226 elements.
Creating vector time with 41226 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.22093 max(Depth.data) = 15.3361
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.22093 max(Depth.data) = 15.3361
 
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/2005/2005021/2005.021.00/hydroscatlog.nc')
Creating vector time with 33494 elements.
Creating vector Seconds with 33494 elements.
Creating vector time with 33494 elements.
Creating vector HundrethsOfSeconds with 33494 elements.
Creating vector time with 33494 elements.
Creating vector Snorm1 with 33494 elements.
Creating vector time with 33494 elements.
Creating vector Snorm2 with 33494 elements.
Creating vector time with 33494 elements.
Creating vector Snorm3 with 33494 elements.
Creating vector time with 33494 elements.
Creating vector Gain_Status_1 with 33494 elements.
Creating vector time with 33494 elements.
Creating vector Gain_Status_2 with 33494 elements.
Creating vector time with 33494 elements.
Creating vector Gain_Status_3 with 33494 elements.
Creating vector time with 33494 elements.
Creating vector RawDepthValue with 33494 elements.
Creating vector time with 33494 elements.
Creating vector RawTempValue with 33494 elements.
Creating vector time with 33494 elements.
Creating vector Temperature with 33494 elements.
Creating vector time with 33494 elements.
Creating vector ErrorValue with 33494 elements.
Creating vector time with 33494 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/hydroscatlog.nc');
 
Processing CTD #1 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/ctdDriver.nc')
Creating vector time with 33413 elements.
Creating vector conductivity with 33413 elements.
Creating vector time with 33413 elements.
Creating vector temperature with 33413 elements.
Creating vector time with 33413 elements.
Creating vector cond_frequency with 33413 elements.
Creating vector time with 33413 elements.
Creating vector temp_frequency with 33413 elements.
Creating vector time with 33413 elements.
Creating vector spare with 33413 elements.
Creating vector time with 33413 elements.
Creating vector humidity with 33413 elements.
Creating vector time with 33413 elements.
Creating vector flow1 with 33413 elements.
Creating vector time with 33413 elements.
Creating vector OBS with 33413 elements.
Creating vector time with 33413 elements.
Creating vector dissolvedO2 with 33413 elements.
Creating vector time with 33413 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/ctdDriver.cfg
Oxygen calibration loaded from CTD config file (current method)
Using constant flow rate offset for oxygen...
 
Processing CTD #2 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/ctdDriver2.nc')
Creating vector time with 33455 elements.
Creating vector conductivity with 33455 elements.
Creating vector time with 33455 elements.
Creating vector temperature with 33455 elements.
Creating vector time with 33455 elements.
Creating vector cond_frequency with 33455 elements.
Creating vector time with 33455 elements.
Creating vector temp_frequency with 33455 elements.
Creating vector time with 33455 elements.
Creating vector flow2 with 33455 elements.
Creating vector time with 33455 elements.
Creating vector spare with 33455 elements.
Creating vector time with 33455 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/ctdDriver2.cfg
 
Processing ISUS data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/isuslog.nc')
Creating vector time with 1075 elements.
Creating vector isusNitrate with 1075 elements.
Creating vector time with 1075 elements.
Creating vector isusTemp with 1075 elements.
Creating vector time with 1075 elements.
Creating vector isusQuality with 1075 elements.
Creating vector time with 1075 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/isuslog.nc');
Total lag applied to nitrate = 6 seconds
 
Processing Biolume data...
[Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 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/2005/2005021/2005.021.00/biolume.nc')
Creating vector time with 8382 elements.
Creating vector rrr with 8382 elements.
Creating vector time with 8382 elements.
Creating vector cal_striing with 8382 elements.
Creating vector time with 8382 elements.
Creating vector pump with 8382 elements.
Creating vector time with 8382 elements.
Creating vector flow with 8382 elements.
Creating vector time with 8382 elements.
Creating vector humidity with 8382 elements.
Creating vector time with 8382 elements.
Creating vector temperature with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_0 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_1 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_2 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_3 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_4 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_5 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_6 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_7 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_8 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_9 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_10 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_11 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_12 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_13 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_14 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_15 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_16 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_17 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_18 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_19 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_20 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_21 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_22 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_23 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_24 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_25 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_26 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_27 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_28 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_29 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_30 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_31 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_32 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_33 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_34 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_35 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_36 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_37 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_38 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_39 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_40 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_41 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_42 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_43 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_44 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_45 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_46 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_47 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_48 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_49 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_50 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_51 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_52 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_53 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_54 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_55 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_56 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_57 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_58 with 8382 elements.
Creating vector time with 8382 elements.
Creating vector raw_59 with 8382 elements.
Creating vector time with 8382 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.00/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/2005/2005021/2005.021.00/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/2005/2005021/2005.021.00/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/2005/2005021/2005.021.00/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_2005.021.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
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Processing AUV mission: 2005.021.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/
Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Processing DVL navigation data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/navigation.nc')
Creating vector time with 11078 elements.
Creating vector mPos_x with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mPos_y with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mDepth with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mGpsNorth with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mGpsEast with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mGpsValid with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mPhi with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mTheta with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mPsi with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mOmega_x with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mOmega_y with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mOmega_z with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mPsaRange with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mAltitude with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mDvlAltitude with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mWaterSpeed with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mDvlValid with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mDvlNewData with 11078 elements.
Creating vector time with 11078 elements.
Creating vector mDeltaT with 11078 elements.
Creating vector time with 11078 elements.
Creating vector nfix with 11078 elements.
Creating vector time with 11078 elements.
Creating vector efix with 11078 elements.
Creating vector time with 11078 elements.
Creating vector filter_north with 11078 elements.
Creating vector time with 11078 elements.
Creating vector filter_east with 11078 elements.
Creating vector time with 11078 elements.
Creating vector filter_depth with 11078 elements.
Creating vector time with 11078 elements.
Creating vector north_current with 11078 elements.
Creating vector time with 11078 elements.
Creating vector east_current with 11078 elements.
Creating vector time with 11078 elements.
Creating vector speed_bias with 11078 elements.
Creating vector time with 11078 elements.
Creating vector heading_bias with 11078 elements.
Creating vector time with 11078 elements.
Creating vector latitude with 11078 elements.
Creating vector time with 11078 elements.
Creating vector longitude with 11078 elements.
Creating vector time with 11078 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/navigation.nc');
processNav(): median of positive valued depths = 8.3512
processNav(): Finding depths less than 58.4585 and times > 0
processNav(): length(Nav.depth) = 11078
processNav(): length(gindx)     = 11078
 
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/2005/2005021/2005.021.01/gps.nc')
Creating vector time with 294 elements.
Creating vector hours with 294 elements.
Creating vector time with 294 elements.
Creating vector minutes with 294 elements.
Creating vector time with 294 elements.
Creating vector seconds with 294 elements.
Creating vector time with 294 elements.
Creating vector centiSeconds with 294 elements.
Creating vector time with 294 elements.
Creating vector latitude with 294 elements.
Creating vector time with 294 elements.
Creating vector longitude with 294 elements.
Creating vector time with 294 elements.
Creating vector quality with 294 elements.
Creating vector time with 294 elements.
Creating vector numberOfSatellites with 294 elements.
Creating vector time with 294 elements.
Creating vector hdop with 294 elements.
Creating vector time with 294 elements.
Creating vector antennaHeight with 294 elements.
Creating vector time with 294 elements.
Creating vector geoHeight with 294 elements.
Creating vector time with 294 elements.
Creating vector dgpsDataAge with 294 elements.
Creating vector time with 294 elements.
Creating vector dgpsRSID with 294 elements.
Creating vector time with 294 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/gps.nc');
 
Processing depth data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/parosci.nc')
Creating vector time with 10946 elements.
Creating vector depth with 10946 elements.
Creating vector time with 10946 elements.
Creating vector temp with 10946 elements.
Creating vector time with 10946 elements.
Creating vector pressure with 10946 elements.
Creating vector time with 10946 elements.
Creating vector temp_period with 10946 elements.
Creating vector time with 10946 elements.
Creating vector pres_period with 10946 elements.
Creating vector time with 10946 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.21894 max(Depth.data) = 14.9706
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.21894 max(Depth.data) = 14.9706
 
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/2005/2005021/2005.021.01/hydroscatlog.nc')
Creating vector time with 8921 elements.
Creating vector Seconds with 8921 elements.
Creating vector time with 8921 elements.
Creating vector HundrethsOfSeconds with 8921 elements.
Creating vector time with 8921 elements.
Creating vector Snorm1 with 8921 elements.
Creating vector time with 8921 elements.
Creating vector Snorm2 with 8921 elements.
Creating vector time with 8921 elements.
Creating vector Snorm3 with 8921 elements.
Creating vector time with 8921 elements.
Creating vector Gain_Status_1 with 8921 elements.
Creating vector time with 8921 elements.
Creating vector Gain_Status_2 with 8921 elements.
Creating vector time with 8921 elements.
Creating vector Gain_Status_3 with 8921 elements.
Creating vector time with 8921 elements.
Creating vector RawDepthValue with 8921 elements.
Creating vector time with 8921 elements.
Creating vector RawTempValue with 8921 elements.
Creating vector time with 8921 elements.
Creating vector Temperature with 8921 elements.
Creating vector time with 8921 elements.
Creating vector ErrorValue with 8921 elements.
Creating vector time with 8921 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/hydroscatlog.nc');
 
Processing CTD #1 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/ctdDriver.nc')
Creating vector time with 8832 elements.
Creating vector conductivity with 8832 elements.
Creating vector time with 8832 elements.
Creating vector temperature with 8832 elements.
Creating vector time with 8832 elements.
Creating vector cond_frequency with 8832 elements.
Creating vector time with 8832 elements.
Creating vector temp_frequency with 8832 elements.
Creating vector time with 8832 elements.
Creating vector spare with 8832 elements.
Creating vector time with 8832 elements.
Creating vector humidity with 8832 elements.
Creating vector time with 8832 elements.
Creating vector flow1 with 8832 elements.
Creating vector time with 8832 elements.
Creating vector OBS with 8832 elements.
Creating vector time with 8832 elements.
Creating vector dissolvedO2 with 8832 elements.
Creating vector time with 8832 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/ctdDriver.cfg
Oxygen calibration loaded from CTD config file (current method)
Using constant flow rate offset for oxygen...
 
Processing CTD #2 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/ctdDriver2.nc')
Creating vector time with 8874 elements.
Creating vector conductivity with 8874 elements.
Creating vector time with 8874 elements.
Creating vector temperature with 8874 elements.
Creating vector time with 8874 elements.
Creating vector cond_frequency with 8874 elements.
Creating vector time with 8874 elements.
Creating vector temp_frequency with 8874 elements.
Creating vector time with 8874 elements.
Creating vector flow2 with 8874 elements.
Creating vector time with 8874 elements.
Creating vector spare with 8874 elements.
Creating vector time with 8874 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/ctdDriver2.cfg
 
Processing ISUS data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/isuslog.nc')
Creating vector time with 279 elements.
Creating vector isusNitrate with 279 elements.
Creating vector time with 279 elements.
Creating vector isusTemp with 279 elements.
Creating vector time with 279 elements.
Creating vector isusQuality with 279 elements.
Creating vector time with 279 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/isuslog.nc');
Total lag applied to nitrate = 6 seconds
 
Processing Biolume data...
[Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 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/2005/2005021/2005.021.01/biolume.nc')
Creating vector time with 2237 elements.
Creating vector rrr with 2237 elements.
Creating vector time with 2237 elements.
Creating vector cal_striing with 2237 elements.
Creating vector time with 2237 elements.
Creating vector pump with 2237 elements.
Creating vector time with 2237 elements.
Creating vector flow with 2237 elements.
Creating vector time with 2237 elements.
Creating vector humidity with 2237 elements.
Creating vector time with 2237 elements.
Creating vector temperature with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_0 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_1 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_2 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_3 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_4 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_5 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_6 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_7 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_8 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_9 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_10 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_11 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_12 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_13 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_14 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_15 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_16 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_17 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_18 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_19 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_20 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_21 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_22 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_23 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_24 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_25 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_26 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_27 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_28 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_29 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_30 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_31 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_32 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_33 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_34 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_35 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_36 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_37 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_38 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_39 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_40 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_41 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_42 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_43 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_44 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_45 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_46 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_47 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_48 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_49 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_50 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_51 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_52 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_53 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_54 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_55 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_56 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_57 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_58 with 2237 elements.
Creating vector time with 2237 elements.
Creating vector raw_59 with 2237 elements.
Creating vector time with 2237 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.01/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/2005/2005021/2005.021.01/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/2005/2005021/2005.021.01/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/2005/2005021/2005.021.01/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_2005.021.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2005.021.02
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/
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/2005/2005021/2005.021.02/navigation.nc')
Creating vector time with 20679 elements.
Creating vector mPos_x with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mPos_y with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mDepth with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mGpsNorth with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mGpsEast with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mGpsValid with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mPhi with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mTheta with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mPsi with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mOmega_x with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mOmega_y with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mOmega_z with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mPsaRange with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mAltitude with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mDvlAltitude with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mWaterSpeed with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mDvlValid with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mDvlNewData with 20679 elements.
Creating vector time with 20679 elements.
Creating vector mDeltaT with 20679 elements.
Creating vector time with 20679 elements.
Creating vector nfix with 20679 elements.
Creating vector time with 20679 elements.
Creating vector efix with 20679 elements.
Creating vector time with 20679 elements.
Creating vector filter_north with 20679 elements.
Creating vector time with 20679 elements.
Creating vector filter_east with 20679 elements.
Creating vector time with 20679 elements.
Creating vector filter_depth with 20679 elements.
Creating vector time with 20679 elements.
Creating vector north_current with 20679 elements.
Creating vector time with 20679 elements.
Creating vector east_current with 20679 elements.
Creating vector time with 20679 elements.
Creating vector speed_bias with 20679 elements.
Creating vector time with 20679 elements.
Creating vector heading_bias with 20679 elements.
Creating vector time with 20679 elements.
Creating vector latitude with 20679 elements.
Creating vector time with 20679 elements.
Creating vector longitude with 20679 elements.
Creating vector time with 20679 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/navigation.nc');
processNav(): median of positive valued depths = 7.3625
processNav(): Finding depths less than 51.5375 and times > 0
processNav(): length(Nav.depth) = 20679
processNav(): length(gindx)     = 20679
 
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/2005/2005021/2005.021.02/gps.nc')
Creating vector time with 303 elements.
Creating vector hours with 303 elements.
Creating vector time with 303 elements.
Creating vector minutes with 303 elements.
Creating vector time with 303 elements.
Creating vector seconds with 303 elements.
Creating vector time with 303 elements.
Creating vector centiSeconds with 303 elements.
Creating vector time with 303 elements.
Creating vector latitude with 303 elements.
Creating vector time with 303 elements.
Creating vector longitude with 303 elements.
Creating vector time with 303 elements.
Creating vector quality with 303 elements.
Creating vector time with 303 elements.
Creating vector numberOfSatellites with 303 elements.
Creating vector time with 303 elements.
Creating vector hdop with 303 elements.
Creating vector time with 303 elements.
Creating vector antennaHeight with 303 elements.
Creating vector time with 303 elements.
Creating vector geoHeight with 303 elements.
Creating vector time with 303 elements.
Creating vector dgpsDataAge with 303 elements.
Creating vector time with 303 elements.
Creating vector dgpsRSID with 303 elements.
Creating vector time with 303 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/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/2005/2005021/2005.021.02/parosci.nc')
Creating vector time with 20421 elements.
Creating vector depth with 20421 elements.
Creating vector time with 20421 elements.
Creating vector temp with 20421 elements.
Creating vector time with 20421 elements.
Creating vector pressure with 20421 elements.
Creating vector time with 20421 elements.
Creating vector temp_period with 20421 elements.
Creating vector time with 20421 elements.
Creating vector pres_period with 20421 elements.
Creating vector time with 20421 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.15751 max(Depth.data) = 15.4167
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.15751 max(Depth.data) = 15.4167
 
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/2005/2005021/2005.021.02/hydroscatlog.nc')
Creating vector time with 16601 elements.
Creating vector Seconds with 16601 elements.
Creating vector time with 16601 elements.
Creating vector HundrethsOfSeconds with 16601 elements.
Creating vector time with 16601 elements.
Creating vector Snorm1 with 16601 elements.
Creating vector time with 16601 elements.
Creating vector Snorm2 with 16601 elements.
Creating vector time with 16601 elements.
Creating vector Snorm3 with 16601 elements.
Creating vector time with 16601 elements.
Creating vector Gain_Status_1 with 16601 elements.
Creating vector time with 16601 elements.
Creating vector Gain_Status_2 with 16601 elements.
Creating vector time with 16601 elements.
Creating vector Gain_Status_3 with 16601 elements.
Creating vector time with 16601 elements.
Creating vector RawDepthValue with 16601 elements.
Creating vector time with 16601 elements.
Creating vector RawTempValue with 16601 elements.
Creating vector time with 16601 elements.
Creating vector Temperature with 16601 elements.
Creating vector time with 16601 elements.
Creating vector ErrorValue with 16601 elements.
Creating vector time with 16601 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/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/2005/2005021/2005.021.02/ctdDriver.nc')
Creating vector time with 16517 elements.
Creating vector conductivity with 16517 elements.
Creating vector time with 16517 elements.
Creating vector temperature with 16517 elements.
Creating vector time with 16517 elements.
Creating vector cond_frequency with 16517 elements.
Creating vector time with 16517 elements.
Creating vector temp_frequency with 16517 elements.
Creating vector time with 16517 elements.
Creating vector spare with 16517 elements.
Creating vector time with 16517 elements.
Creating vector humidity with 16517 elements.
Creating vector time with 16517 elements.
Creating vector flow1 with 16517 elements.
Creating vector time with 16517 elements.
Creating vector OBS with 16517 elements.
Creating vector time with 16517 elements.
Creating vector dissolvedO2 with 16517 elements.
Creating vector time with 16517 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/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/2005/2005021/2005.021.02/ctdDriver2.nc')
Creating vector time with 16558 elements.
Creating vector conductivity with 16558 elements.
Creating vector time with 16558 elements.
Creating vector temperature with 16558 elements.
Creating vector time with 16558 elements.
Creating vector cond_frequency with 16558 elements.
Creating vector time with 16558 elements.
Creating vector temp_frequency with 16558 elements.
Creating vector time with 16558 elements.
Creating vector flow2 with 16558 elements.
Creating vector time with 16558 elements.
Creating vector spare with 16558 elements.
Creating vector time with 16558 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/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/2005/2005021/2005.021.02/isuslog.nc')
Creating vector time with 527 elements.
Creating vector isusNitrate with 527 elements.
Creating vector time with 527 elements.
Creating vector isusTemp with 527 elements.
Creating vector time with 527 elements.
Creating vector isusQuality with 527 elements.
Creating vector time with 527 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/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/2005/2005021/2005.021.02/biolume.nc')
Creating vector time with 4158 elements.
Creating vector rrr with 4158 elements.
Creating vector time with 4158 elements.
Creating vector cal_striing with 4158 elements.
Creating vector time with 4158 elements.
Creating vector pump with 4158 elements.
Creating vector time with 4158 elements.
Creating vector flow with 4158 elements.
Creating vector time with 4158 elements.
Creating vector humidity with 4158 elements.
Creating vector time with 4158 elements.
Creating vector temperature with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_0 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_1 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_2 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_3 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_4 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_5 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_6 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_7 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_8 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_9 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_10 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_11 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_12 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_13 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_14 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_15 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_16 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_17 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_18 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_19 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_20 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_21 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_22 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_23 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_24 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_25 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_26 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_27 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_28 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_29 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_30 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_31 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_32 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_33 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_34 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_35 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_36 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_37 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_38 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_39 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_40 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_41 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_42 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_43 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_44 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_45 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_46 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_47 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_48 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_49 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_50 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_51 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_52 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_53 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_54 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_55 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_56 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_57 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_58 with 4158 elements.
Creating vector time with 4158 elements.
Creating vector raw_59 with 4158 elements.
Creating vector time with 4158 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.02/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/2005/2005021/2005.021.02/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/2005/2005021/2005.021.02/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/2005/2005021/2005.021.02/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_2005.021.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2005.021.03
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/
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/2005/2005021/2005.021.03/navigation.nc')
Creating vector time with 41364 elements.
Creating vector mPos_x with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mPos_y with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mDepth with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mGpsNorth with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mGpsEast with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mGpsValid with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mPhi with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mTheta with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mPsi with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mOmega_x with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mOmega_y with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mOmega_z with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mPsaRange with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mAltitude with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mDvlAltitude with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mWaterSpeed with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mDvlValid with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mDvlNewData with 41364 elements.
Creating vector time with 41364 elements.
Creating vector mDeltaT with 41364 elements.
Creating vector time with 41364 elements.
Creating vector nfix with 41364 elements.
Creating vector time with 41364 elements.
Creating vector efix with 41364 elements.
Creating vector time with 41364 elements.
Creating vector filter_north with 41364 elements.
Creating vector time with 41364 elements.
Creating vector filter_east with 41364 elements.
Creating vector time with 41364 elements.
Creating vector filter_depth with 41364 elements.
Creating vector time with 41364 elements.
Creating vector north_current with 41364 elements.
Creating vector time with 41364 elements.
Creating vector east_current with 41364 elements.
Creating vector time with 41364 elements.
Creating vector speed_bias with 41364 elements.
Creating vector time with 41364 elements.
Creating vector heading_bias with 41364 elements.
Creating vector time with 41364 elements.
Creating vector latitude with 41364 elements.
Creating vector time with 41364 elements.
Creating vector longitude with 41364 elements.
Creating vector time with 41364 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/navigation.nc');
processNav(): median of positive valued depths = 7.2429
processNav(): Finding depths less than 50.7004 and times > 0
processNav(): length(Nav.depth) = 41364
processNav(): length(gindx)     = 41364
 
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/2005/2005021/2005.021.03/gps.nc')
Creating vector time with 490 elements.
Creating vector hours with 490 elements.
Creating vector time with 490 elements.
Creating vector minutes with 490 elements.
Creating vector time with 490 elements.
Creating vector seconds with 490 elements.
Creating vector time with 490 elements.
Creating vector centiSeconds with 490 elements.
Creating vector time with 490 elements.
Creating vector latitude with 490 elements.
Creating vector time with 490 elements.
Creating vector longitude with 490 elements.
Creating vector time with 490 elements.
Creating vector quality with 490 elements.
Creating vector time with 490 elements.
Creating vector numberOfSatellites with 490 elements.
Creating vector time with 490 elements.
Creating vector hdop with 490 elements.
Creating vector time with 490 elements.
Creating vector antennaHeight with 490 elements.
Creating vector time with 490 elements.
Creating vector geoHeight with 490 elements.
Creating vector time with 490 elements.
Creating vector dgpsDataAge with 490 elements.
Creating vector time with 490 elements.
Creating vector dgpsRSID with 490 elements.
Creating vector time with 490 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/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/2005/2005021/2005.021.03/parosci.nc')
Creating vector time with 40744 elements.
Creating vector depth with 40744 elements.
Creating vector time with 40744 elements.
Creating vector temp with 40744 elements.
Creating vector time with 40744 elements.
Creating vector pressure with 40744 elements.
Creating vector time with 40744 elements.
Creating vector temp_period with 40744 elements.
Creating vector time with 40744 elements.
Creating vector pres_period with 40744 elements.
Creating vector time with 40744 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.11277 max(Depth.data) = 15.4391
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.11277 max(Depth.data) = 15.4391
 
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/2005/2005021/2005.021.03/hydroscatlog.nc')
Creating vector time with 33143 elements.
Creating vector Seconds with 33143 elements.
Creating vector time with 33143 elements.
Creating vector HundrethsOfSeconds with 33143 elements.
Creating vector time with 33143 elements.
Creating vector Snorm1 with 33143 elements.
Creating vector time with 33143 elements.
Creating vector Snorm2 with 33143 elements.
Creating vector time with 33143 elements.
Creating vector Snorm3 with 33143 elements.
Creating vector time with 33143 elements.
Creating vector Gain_Status_1 with 33143 elements.
Creating vector time with 33143 elements.
Creating vector Gain_Status_2 with 33143 elements.
Creating vector time with 33143 elements.
Creating vector Gain_Status_3 with 33143 elements.
Creating vector time with 33143 elements.
Creating vector RawDepthValue with 33143 elements.
Creating vector time with 33143 elements.
Creating vector RawTempValue with 33143 elements.
Creating vector time with 33143 elements.
Creating vector Temperature with 33143 elements.
Creating vector time with 33143 elements.
Creating vector ErrorValue with 33143 elements.
Creating vector time with 33143 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/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/2005/2005021/2005.021.03/ctdDriver.nc')
Creating vector time with 33104 elements.
Creating vector conductivity with 33104 elements.
Creating vector time with 33104 elements.
Creating vector temperature with 33104 elements.
Creating vector time with 33104 elements.
Creating vector cond_frequency with 33104 elements.
Creating vector time with 33104 elements.
Creating vector temp_frequency with 33104 elements.
Creating vector time with 33104 elements.
Creating vector spare with 33104 elements.
Creating vector time with 33104 elements.
Creating vector humidity with 33104 elements.
Creating vector time with 33104 elements.
Creating vector flow1 with 33104 elements.
Creating vector time with 33104 elements.
Creating vector OBS with 33104 elements.
Creating vector time with 33104 elements.
Creating vector dissolvedO2 with 33104 elements.
Creating vector time with 33104 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/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/2005/2005021/2005.021.03/ctdDriver2.nc')
Creating vector time with 33144 elements.
Creating vector conductivity with 33144 elements.
Creating vector time with 33144 elements.
Creating vector temperature with 33144 elements.
Creating vector time with 33144 elements.
Creating vector cond_frequency with 33144 elements.
Creating vector time with 33144 elements.
Creating vector temp_frequency with 33144 elements.
Creating vector time with 33144 elements.
Creating vector flow2 with 33144 elements.
Creating vector time with 33144 elements.
Creating vector spare with 33144 elements.
Creating vector time with 33144 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/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/2005/2005021/2005.021.03/isuslog.nc')
Creating vector time with 1063 elements.
Creating vector isusNitrate with 1063 elements.
Creating vector time with 1063 elements.
Creating vector isusTemp with 1063 elements.
Creating vector time with 1063 elements.
Creating vector isusQuality with 1063 elements.
Creating vector time with 1063 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/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/2005/2005021/2005.021.03/biolume.nc')
Creating vector time with 8295 elements.
Creating vector rrr with 8295 elements.
Creating vector time with 8295 elements.
Creating vector cal_striing with 8295 elements.
Creating vector time with 8295 elements.
Creating vector pump with 8295 elements.
Creating vector time with 8295 elements.
Creating vector flow with 8295 elements.
Creating vector time with 8295 elements.
Creating vector humidity with 8295 elements.
Creating vector time with 8295 elements.
Creating vector temperature with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_0 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_1 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_2 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_3 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_4 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_5 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_6 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_7 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_8 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_9 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_10 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_11 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_12 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_13 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_14 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_15 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_16 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_17 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_18 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_19 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_20 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_21 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_22 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_23 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_24 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_25 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_26 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_27 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_28 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_29 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_30 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_31 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_32 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_33 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_34 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_35 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_36 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_37 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_38 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_39 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_40 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_41 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_42 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_43 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_44 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_45 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_46 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_47 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_48 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_49 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_50 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_51 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_52 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_53 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_54 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_55 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_56 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_57 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_58 with 8295 elements.
Creating vector time with 8295 elements.
Creating vector raw_59 with 8295 elements.
Creating vector time with 8295 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.03/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/2005/2005021/2005.021.03/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/2005/2005021/2005.021.03/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/2005/2005021/2005.021.03/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_2005.021.03.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2005.021.04
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/
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/2005/2005021/2005.021.04/navigation.nc')
Creating vector time with 20433 elements.
Creating vector mPos_x with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mPos_y with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mDepth with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mGpsNorth with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mGpsEast with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mGpsValid with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mPhi with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mTheta with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mPsi with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mOmega_x with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mOmega_y with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mOmega_z with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mPsaRange with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mAltitude with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mDvlAltitude with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mWaterSpeed with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mDvlValid with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mDvlNewData with 20433 elements.
Creating vector time with 20433 elements.
Creating vector mDeltaT with 20433 elements.
Creating vector time with 20433 elements.
Creating vector nfix with 20433 elements.
Creating vector time with 20433 elements.
Creating vector efix with 20433 elements.
Creating vector time with 20433 elements.
Creating vector filter_north with 20433 elements.
Creating vector time with 20433 elements.
Creating vector filter_east with 20433 elements.
Creating vector time with 20433 elements.
Creating vector filter_depth with 20433 elements.
Creating vector time with 20433 elements.
Creating vector north_current with 20433 elements.
Creating vector time with 20433 elements.
Creating vector east_current with 20433 elements.
Creating vector time with 20433 elements.
Creating vector speed_bias with 20433 elements.
Creating vector time with 20433 elements.
Creating vector heading_bias with 20433 elements.
Creating vector time with 20433 elements.
Creating vector latitude with 20433 elements.
Creating vector time with 20433 elements.
Creating vector longitude with 20433 elements.
Creating vector time with 20433 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/navigation.nc');
processNav(): median of positive valued depths = 7.033
processNav(): Finding depths less than 49.2313 and times > 0
processNav(): length(Nav.depth) = 20433
processNav(): length(gindx)     = 20433
 
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/2005/2005021/2005.021.04/gps.nc')
Creating vector time with 193 elements.
Creating vector hours with 193 elements.
Creating vector time with 193 elements.
Creating vector minutes with 193 elements.
Creating vector time with 193 elements.
Creating vector seconds with 193 elements.
Creating vector time with 193 elements.
Creating vector centiSeconds with 193 elements.
Creating vector time with 193 elements.
Creating vector latitude with 193 elements.
Creating vector time with 193 elements.
Creating vector longitude with 193 elements.
Creating vector time with 193 elements.
Creating vector quality with 193 elements.
Creating vector time with 193 elements.
Creating vector numberOfSatellites with 193 elements.
Creating vector time with 193 elements.
Creating vector hdop with 193 elements.
Creating vector time with 193 elements.
Creating vector antennaHeight with 193 elements.
Creating vector time with 193 elements.
Creating vector geoHeight with 193 elements.
Creating vector time with 193 elements.
Creating vector dgpsDataAge with 193 elements.
Creating vector time with 193 elements.
Creating vector dgpsRSID with 193 elements.
Creating vector time with 193 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/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/2005/2005021/2005.021.04/parosci.nc')
Creating vector time with 20043 elements.
Creating vector depth with 20043 elements.
Creating vector time with 20043 elements.
Creating vector temp with 20043 elements.
Creating vector time with 20043 elements.
Creating vector pressure with 20043 elements.
Creating vector time with 20043 elements.
Creating vector temp_period with 20043 elements.
Creating vector time with 20043 elements.
Creating vector pres_period with 20043 elements.
Creating vector time with 20043 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.16588 max(Depth.data) = 15.3478
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.16588 max(Depth.data) = 15.3478
 
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/2005/2005021/2005.021.04/hydroscatlog.nc')
Creating vector time with 16402 elements.
Creating vector Seconds with 16402 elements.
Creating vector time with 16402 elements.
Creating vector HundrethsOfSeconds with 16402 elements.
Creating vector time with 16402 elements.
Creating vector Snorm1 with 16402 elements.
Creating vector time with 16402 elements.
Creating vector Snorm2 with 16402 elements.
Creating vector time with 16402 elements.
Creating vector Snorm3 with 16402 elements.
Creating vector time with 16402 elements.
Creating vector Gain_Status_1 with 16402 elements.
Creating vector time with 16402 elements.
Creating vector Gain_Status_2 with 16402 elements.
Creating vector time with 16402 elements.
Creating vector Gain_Status_3 with 16402 elements.
Creating vector time with 16402 elements.
Creating vector RawDepthValue with 16402 elements.
Creating vector time with 16402 elements.
Creating vector RawTempValue with 16402 elements.
Creating vector time with 16402 elements.
Creating vector Temperature with 16402 elements.
Creating vector time with 16402 elements.
Creating vector ErrorValue with 16402 elements.
Creating vector time with 16402 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/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/2005/2005021/2005.021.04/ctdDriver.nc')
Creating vector time with 16353 elements.
Creating vector conductivity with 16353 elements.
Creating vector time with 16353 elements.
Creating vector temperature with 16353 elements.
Creating vector time with 16353 elements.
Creating vector cond_frequency with 16353 elements.
Creating vector time with 16353 elements.
Creating vector temp_frequency with 16353 elements.
Creating vector time with 16353 elements.
Creating vector spare with 16353 elements.
Creating vector time with 16353 elements.
Creating vector humidity with 16353 elements.
Creating vector time with 16353 elements.
Creating vector flow1 with 16353 elements.
Creating vector time with 16353 elements.
Creating vector OBS with 16353 elements.
Creating vector time with 16353 elements.
Creating vector dissolvedO2 with 16353 elements.
Creating vector time with 16353 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/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/2005/2005021/2005.021.04/ctdDriver2.nc')
Creating vector time with 16395 elements.
Creating vector conductivity with 16395 elements.
Creating vector time with 16395 elements.
Creating vector temperature with 16395 elements.
Creating vector time with 16395 elements.
Creating vector cond_frequency with 16395 elements.
Creating vector time with 16395 elements.
Creating vector temp_frequency with 16395 elements.
Creating vector time with 16395 elements.
Creating vector flow2 with 16395 elements.
Creating vector time with 16395 elements.
Creating vector spare with 16395 elements.
Creating vector time with 16395 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/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/2005/2005021/2005.021.04/isuslog.nc')
Creating vector time with 520 elements.
Creating vector isusNitrate with 520 elements.
Creating vector time with 520 elements.
Creating vector isusTemp with 520 elements.
Creating vector time with 520 elements.
Creating vector isusQuality with 520 elements.
Creating vector time with 520 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/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/2005/2005021/2005.021.04/biolume.nc')
Creating vector time with 4108 elements.
Creating vector rrr with 4108 elements.
Creating vector time with 4108 elements.
Creating vector cal_striing with 4108 elements.
Creating vector time with 4108 elements.
Creating vector pump with 4108 elements.
Creating vector time with 4108 elements.
Creating vector flow with 4108 elements.
Creating vector time with 4108 elements.
Creating vector humidity with 4108 elements.
Creating vector time with 4108 elements.
Creating vector temperature with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_0 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_1 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_2 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_3 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_4 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_5 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_6 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_7 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_8 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_9 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_10 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_11 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_12 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_13 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_14 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_15 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_16 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_17 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_18 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_19 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_20 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_21 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_22 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_23 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_24 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_25 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_26 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_27 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_28 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_29 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_30 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_31 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_32 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_33 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_34 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_35 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_36 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_37 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_38 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_39 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_40 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_41 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_42 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_43 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_44 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_45 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_46 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_47 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_48 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_49 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_50 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_51 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_52 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_53 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_54 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_55 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_56 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_57 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_58 with 4108 elements.
Creating vector time with 4108 elements.
Creating vector raw_59 with 4108 elements.
Creating vector time with 4108 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005021/2005.021.04/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/2005/2005021/2005.021.04/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/2005/2005021/2005.021.04/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/2005/2005021/2005.021.04/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_2005.021.04.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_2005.021.00.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.021.01.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.021.02.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.021.03.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.021.04.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 19 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_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 = 340 Gridding with nix = 1020, iZ = 28
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
[Warning: Duplicate data points have been detected and removed - corresponding
values have been averaged.] 
[> In griddata>useScatteredInterp (line 185)
  In griddata (line 126)
  In plot_sections (line 274)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
   N
[Warning: Duplicate data points have been detected and removed - corresponding
values have been averaged.] 
[> In griddata>useScatteredInterp (line 185)
  In griddata (line 126)
  In plot_sections (line 304)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
   BL
   BLflow
   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
  cvarname = 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 135292 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 135292 points from grid Monterey25.grd (2876 x 2447)
Getting short wave radiation data from M1 for little plot above the biolume section plot
Creating vector TIME with 119044 elements.

ds = 

  cfdataset with properties:

       netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset]
    variables: {16x1 cell}

SWR data read from OPeNDAP has time range: 01/21/2005 05:30  to 01/21/2005 15:29 

swr =

    1.7862
    1.6000
   14.3054
  175.3406
  305.3690
  454.9303
  442.5227
  564.8325
  503.4558
  412.2416
  208.3377

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2005021_GulperTimes.txt && touch ../results/2005021_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/2005/2005021/2005.021.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005021/2005.021.00/syslog -startEsecs 1106345603.9273 -surveyName Dorado389_2005_021_00_021_04 >> ../results/2005021_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005021_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/2005/2005021/2005.021.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005021/2005.021.01/syslog -startEsecs 1106345603.9273 -surveyName Dorado389_2005_021_00_021_04 >> ../results/2005021_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005021_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/2005/2005021/2005.021.02/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005021/2005.021.02/syslog -startEsecs 1106345603.9273 -surveyName Dorado389_2005_021_00_021_04 >> ../results/2005021_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005021_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/2005/2005021/2005.021.03/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005021/2005.021.03/syslog -startEsecs 1106345603.9273 -surveyName Dorado389_2005_021_00_021_04 >> ../results/2005021_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005021_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/2005/2005021/2005.021.04/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005021/2005.021.04/syslog -startEsecs 1106345603.9273 -surveyName Dorado389_2005_021_00_021_04 >> ../results/2005021_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005021_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_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
  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_2005_021_00_021_04_2column.png
Elapsed time to save image: 8 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_2005_021_00_021_04_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_2005_021_00_021_04_lopc.png
Elapsed time to save image: 8 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_2005_021_00_021_04_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_2column.png...
Copied to /mbari/AUVCTD/surveys/2005/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_biolume.png...
Copied to /mbari/AUVCTD/surveys/2005/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_lopc.png...
Copied to /mbari/AUVCTD/surveys/2005/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2005/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2005/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2005/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_2005_021_00_021_04_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_021_00_021_04_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2005/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_2005_021_00_021_04_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_021_00_021_04_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2005/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);
Could not do interp1: The grid vectors must contain unique points.
Did not write KML for this variable.  Rethrowing error.
Could not create .kmz for Nitrate                    
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_2005_021_00_021_04_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_021_00_021_04_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2005/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);
Could not do interp1: The grid vectors must contain unique points.
Did not write KML for this variable.  Rethrowing error.
Could not create .kmz for Optical Backscatter @470 nm
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath);
Could not do interp1: The grid vectors must contain unique points.
Did not write KML for this variable.  Rethrowing error.
Could not create .kmz for Optical Backscatter @676 nm
KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath);
Could not do interp1: The grid vectors must contain unique points.
Did not write KML for this variable.  Rethrowing error.
Could not create .kmz for Chlorophyll Fluorescence   
KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_021_00_021_04_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_021_00_021_04_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2005/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_2005_021_00_021_04_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_021_00_021_04_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2005/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2005_021_00_021_04.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04.kml...
Copied to /mbari/AUVCTD/surveys/2005/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_021_00_021_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_2005_021_00_021_04.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
75459 NaNs found in bbpBlue.  Interpolating anyway.
71927 NaNs found in bbpRed.  Interpolating anyway.
Encountered 2 NaN values in array of lon that is 3463 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 3461 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 3461 are not equal to number of Lat lon points = 3463
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_2005_021_00_021_04.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04.txt...
Copied to /mbari/AUVCTD/surveys/2005/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_Gulper.txt...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2005/odv/
cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
75459 NaNs found in bbpBlue.  Interpolating anyway.
71927 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_decim.nc...
Copied to /mbari/AUVCTD/surveys/2005/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_2005_021_00_021_04.nc...
Copied to /mbari/AUVCTD/surveys/2005/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2005/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_021_00_021_04.mat...
Copied to /mbari/AUVCTD/surveys/2005/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2005_021_00_021_04 processed" mccann@mbari.org < mail_Dorado389_2005_021_00_021_04.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.021.00.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.021.01.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.021.02.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.021.03.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.021.04.mat
Processing time: 92 seconds