Execution of AUVprocess_main version 1.86 at 2018-05-31T16:39:24Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2005, ['332.00';'332.01';'332.02';'332.03';'332.04'], '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: 2005.332.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/
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/2005/2005332/2005.332.00/navigation.nc')
Creating vector time with 4059 elements.
Creating vector mPos_x with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mPos_y with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mDepth with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mGpsNorth with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mGpsEast with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mGpsValid with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mPhi with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mTheta with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mPsi with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mOmega_x with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mOmega_y with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mOmega_z with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mPsaRange with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mAltitude with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mDvlAltitude with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mWaterSpeed with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mDvlValid with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mDvlNewData with 4059 elements.
Creating vector time with 4059 elements.
Creating vector mDeltaT with 4059 elements.
Creating vector time with 4059 elements.
Creating vector nfix with 4059 elements.
Creating vector time with 4059 elements.
Creating vector efix with 4059 elements.
Creating vector time with 4059 elements.
Creating vector filter_north with 4059 elements.
Creating vector time with 4059 elements.
Creating vector filter_east with 4059 elements.
Creating vector time with 4059 elements.
Creating vector filter_depth with 4059 elements.
Creating vector time with 4059 elements.
Creating vector north_current with 4059 elements.
Creating vector time with 4059 elements.
Creating vector east_current with 4059 elements.
Creating vector time with 4059 elements.
Creating vector speed_bias with 4059 elements.
Creating vector time with 4059 elements.
Creating vector heading_bias with 4059 elements.
Creating vector time with 4059 elements.
Creating vector latitude with 4059 elements.
Creating vector time with 4059 elements.
Creating vector longitude with 4059 elements.
Creating vector time with 4059 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/navigation.nc');
processNav(): median of positive valued depths = 20.3672
processNav(): Finding depths less than 142.5702 and times > 0
processNav(): length(Nav.depth) = 4059
processNav(): length(gindx)     = 4059
 
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/2005/2005332/2005.332.00/gps.nc')
Creating vector time with 125 elements.
Creating vector hours with 125 elements.
Creating vector time with 125 elements.
Creating vector minutes with 125 elements.
Creating vector time with 125 elements.
Creating vector seconds with 125 elements.
Creating vector time with 125 elements.
Creating vector centiSeconds with 125 elements.
Creating vector time with 125 elements.
Creating vector latitude with 125 elements.
Creating vector time with 125 elements.
Creating vector longitude with 125 elements.
Creating vector time with 125 elements.
Creating vector quality with 125 elements.
Creating vector time with 125 elements.
Creating vector numberOfSatellites with 125 elements.
Creating vector time with 125 elements.
Creating vector hdop with 125 elements.
Creating vector time with 125 elements.
Creating vector antennaHeight with 125 elements.
Creating vector time with 125 elements.
Creating vector geoHeight with 125 elements.
Creating vector time with 125 elements.
Creating vector dgpsDataAge with 125 elements.
Creating vector time with 125 elements.
Creating vector dgpsRSID with 125 elements.
Creating vector time with 125 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/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/2005/2005332/2005.332.00/parosci.nc')
Creating vector time with 8889 elements.
Creating vector depth with 8889 elements.
Creating vector time with 8889 elements.
Creating vector temp with 8889 elements.
Creating vector time with 8889 elements.
Creating vector pressure with 8889 elements.
Creating vector time with 8889 elements.
Creating vector temp_period with 8889 elements.
Creating vector time with 8889 elements.
Creating vector pres_period with 8889 elements.
Creating vector time with 8889 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.14102 max(Depth.data) = 41.8095
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.14102 max(Depth.data) = 41.8095
 
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/2005/2005332/2005.332.00/hydroscatlog.nc')
Creating vector time with 3303 elements.
Creating vector Seconds with 3303 elements.
Creating vector time with 3303 elements.
Creating vector HundrethsOfSeconds with 3303 elements.
Creating vector time with 3303 elements.
Creating vector Snorm1 with 3303 elements.
Creating vector time with 3303 elements.
Creating vector Snorm2 with 3303 elements.
Creating vector time with 3303 elements.
Creating vector Snorm3 with 3303 elements.
Creating vector time with 3303 elements.
Creating vector Gain_Status_1 with 3303 elements.
Creating vector time with 3303 elements.
Creating vector Gain_Status_2 with 3303 elements.
Creating vector time with 3303 elements.
Creating vector Gain_Status_3 with 3303 elements.
Creating vector time with 3303 elements.
Creating vector RawDepthValue with 3303 elements.
Creating vector time with 3303 elements.
Creating vector RawTempValue with 3303 elements.
Creating vector time with 3303 elements.
Creating vector Temperature with 3303 elements.
Creating vector time with 3303 elements.
Creating vector ErrorValue with 3303 elements.
Creating vector time with 3303 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/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/2005/2005332/2005.332.00/ctdDriver.nc')
Creating vector time with 3220 elements.
Creating vector conductivity with 3220 elements.
Creating vector time with 3220 elements.
Creating vector temperature with 3220 elements.
Creating vector time with 3220 elements.
Creating vector cond_frequency with 3220 elements.
Creating vector time with 3220 elements.
Creating vector temp_frequency with 3220 elements.
Creating vector time with 3220 elements.
Creating vector spare with 3220 elements.
Creating vector time with 3220 elements.
Creating vector humidity with 3220 elements.
Creating vector time with 3220 elements.
Creating vector flow1 with 3220 elements.
Creating vector time with 3220 elements.
Creating vector OBS with 3220 elements.
Creating vector time with 3220 elements.
Creating vector dissolvedO2 with 3220 elements.
Creating vector time with 3220 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/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/2005/2005332/2005.332.00/ctdDriver2.nc')
Creating vector time with 3217 elements.
Creating vector conductivity with 3217 elements.
Creating vector time with 3217 elements.
Creating vector temperature with 3217 elements.
Creating vector time with 3217 elements.
Creating vector cond_frequency with 3217 elements.
Creating vector time with 3217 elements.
Creating vector temp_frequency with 3217 elements.
Creating vector time with 3217 elements.
Creating vector flow2 with 3217 elements.
Creating vector time with 3217 elements.
Creating vector spare with 3217 elements.
Creating vector time with 3217 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/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/2005/2005332/2005.332.00/isuslog.nc')
Creating vector time with 472 elements.
Creating vector isusNitrate with 472 elements.
Creating vector time with 472 elements.
Creating vector isusTemp with 472 elements.
Creating vector time with 472 elements.
Creating vector isusQuality with 472 elements.
Creating vector time with 472 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/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/2005/2005332/2005.332.00/biolume.nc')
Creating vector time with 832 elements.
Creating vector rrr with 832 elements.
Creating vector time with 832 elements.
Creating vector cal_striing with 832 elements.
Creating vector time with 832 elements.
Creating vector pump with 832 elements.
Creating vector time with 832 elements.
Creating vector flow with 832 elements.
Creating vector time with 832 elements.
Creating vector humidity with 832 elements.
Creating vector time with 832 elements.
Creating vector temperature with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_0 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_1 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_2 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_3 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_4 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_5 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_6 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_7 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_8 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_9 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_10 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_11 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_12 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_13 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_14 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_15 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_16 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_17 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_18 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_19 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_20 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_21 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_22 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_23 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_24 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_25 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_26 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_27 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_28 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_29 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_30 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_31 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_32 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_33 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_34 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_35 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_36 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_37 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_38 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_39 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_40 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_41 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_42 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_43 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_44 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_45 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_46 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_47 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_48 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_49 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_50 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_51 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_52 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_53 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_54 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_55 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_56 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_57 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_58 with 832 elements.
Creating vector time with 832 elements.
Creating vector raw_59 with 832 elements.
Creating vector time with 832 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.00/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/2005/2005332/2005.332.00/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/2005/2005332/2005.332.00/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/2005/2005332/2005.332.00/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/2005/2005332/2005.332.00/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_2005.332.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
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Processing AUV mission: 2005.332.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/
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/2005/2005332/2005.332.01/navigation.nc')
Creating vector time with 3691 elements.
Creating vector mPos_x with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mPos_y with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mDepth with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mGpsNorth with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mGpsEast with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mGpsValid with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mPhi with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mTheta with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mPsi with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mOmega_x with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mOmega_y with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mOmega_z with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mPsaRange with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mAltitude with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mDvlAltitude with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mWaterSpeed with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mDvlValid with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mDvlNewData with 3691 elements.
Creating vector time with 3691 elements.
Creating vector mDeltaT with 3691 elements.
Creating vector time with 3691 elements.
Creating vector nfix with 3691 elements.
Creating vector time with 3691 elements.
Creating vector efix with 3691 elements.
Creating vector time with 3691 elements.
Creating vector filter_north with 3691 elements.
Creating vector time with 3691 elements.
Creating vector filter_east with 3691 elements.
Creating vector time with 3691 elements.
Creating vector filter_depth with 3691 elements.
Creating vector time with 3691 elements.
Creating vector north_current with 3691 elements.
Creating vector time with 3691 elements.
Creating vector east_current with 3691 elements.
Creating vector time with 3691 elements.
Creating vector speed_bias with 3691 elements.
Creating vector time with 3691 elements.
Creating vector heading_bias with 3691 elements.
Creating vector time with 3691 elements.
Creating vector latitude with 3691 elements.
Creating vector time with 3691 elements.
Creating vector longitude with 3691 elements.
Creating vector time with 3691 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/navigation.nc');
processNav(): median of positive valued depths = 19.6306
processNav(): Finding depths less than 137.4145 and times > 0
processNav(): length(Nav.depth) = 3691
processNav(): length(gindx)     = 3691
 
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/2005/2005332/2005.332.01/gps.nc')
Creating vector time with 114 elements.
Creating vector hours with 114 elements.
Creating vector time with 114 elements.
Creating vector minutes with 114 elements.
Creating vector time with 114 elements.
Creating vector seconds with 114 elements.
Creating vector time with 114 elements.
Creating vector centiSeconds with 114 elements.
Creating vector time with 114 elements.
Creating vector latitude with 114 elements.
Creating vector time with 114 elements.
Creating vector longitude with 114 elements.
Creating vector time with 114 elements.
Creating vector quality with 114 elements.
Creating vector time with 114 elements.
Creating vector numberOfSatellites with 114 elements.
Creating vector time with 114 elements.
Creating vector hdop with 114 elements.
Creating vector time with 114 elements.
Creating vector antennaHeight with 114 elements.
Creating vector time with 114 elements.
Creating vector geoHeight with 114 elements.
Creating vector time with 114 elements.
Creating vector dgpsDataAge with 114 elements.
Creating vector time with 114 elements.
Creating vector dgpsRSID with 114 elements.
Creating vector time with 114 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/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/2005/2005332/2005.332.01/parosci.nc')
Creating vector time with 8076 elements.
Creating vector depth with 8076 elements.
Creating vector time with 8076 elements.
Creating vector temp with 8076 elements.
Creating vector time with 8076 elements.
Creating vector pressure with 8076 elements.
Creating vector time with 8076 elements.
Creating vector temp_period with 8076 elements.
Creating vector time with 8076 elements.
Creating vector pres_period with 8076 elements.
Creating vector time with 8076 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.2815 max(Depth.data) = 42.5293
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.2815 max(Depth.data) = 42.5293
 
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/2005/2005332/2005.332.01/hydroscatlog.nc')
Creating vector time with 3011 elements.
Creating vector Seconds with 3011 elements.
Creating vector time with 3011 elements.
Creating vector HundrethsOfSeconds with 3011 elements.
Creating vector time with 3011 elements.
Creating vector Snorm1 with 3011 elements.
Creating vector time with 3011 elements.
Creating vector Snorm2 with 3011 elements.
Creating vector time with 3011 elements.
Creating vector Snorm3 with 3011 elements.
Creating vector time with 3011 elements.
Creating vector Gain_Status_1 with 3011 elements.
Creating vector time with 3011 elements.
Creating vector Gain_Status_2 with 3011 elements.
Creating vector time with 3011 elements.
Creating vector Gain_Status_3 with 3011 elements.
Creating vector time with 3011 elements.
Creating vector RawDepthValue with 3011 elements.
Creating vector time with 3011 elements.
Creating vector RawTempValue with 3011 elements.
Creating vector time with 3011 elements.
Creating vector Temperature with 3011 elements.
Creating vector time with 3011 elements.
Creating vector ErrorValue with 3011 elements.
Creating vector time with 3011 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/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/2005/2005332/2005.332.01/ctdDriver.nc')
Creating vector time with 2920 elements.
Creating vector conductivity with 2920 elements.
Creating vector time with 2920 elements.
Creating vector temperature with 2920 elements.
Creating vector time with 2920 elements.
Creating vector cond_frequency with 2920 elements.
Creating vector time with 2920 elements.
Creating vector temp_frequency with 2920 elements.
Creating vector time with 2920 elements.
Creating vector spare with 2920 elements.
Creating vector time with 2920 elements.
Creating vector humidity with 2920 elements.
Creating vector time with 2920 elements.
Creating vector flow1 with 2920 elements.
Creating vector time with 2920 elements.
Creating vector OBS with 2920 elements.
Creating vector time with 2920 elements.
Creating vector dissolvedO2 with 2920 elements.
Creating vector time with 2920 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/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/2005/2005332/2005.332.01/ctdDriver2.nc')
Creating vector time with 2915 elements.
Creating vector conductivity with 2915 elements.
Creating vector time with 2915 elements.
Creating vector temperature with 2915 elements.
Creating vector time with 2915 elements.
Creating vector cond_frequency with 2915 elements.
Creating vector time with 2915 elements.
Creating vector temp_frequency with 2915 elements.
Creating vector time with 2915 elements.
Creating vector flow2 with 2915 elements.
Creating vector time with 2915 elements.
Creating vector spare with 2915 elements.
Creating vector time with 2915 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/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/2005/2005332/2005.332.01/isuslog.nc')
Creating vector time with 425 elements.
Creating vector isusNitrate with 425 elements.
Creating vector time with 425 elements.
Creating vector isusTemp with 425 elements.
Creating vector time with 425 elements.
Creating vector isusQuality with 425 elements.
Creating vector time with 425 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/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/2005/2005332/2005.332.01/biolume.nc')
Creating vector time with 758 elements.
Creating vector rrr with 758 elements.
Creating vector time with 758 elements.
Creating vector cal_striing with 758 elements.
Creating vector time with 758 elements.
Creating vector pump with 758 elements.
Creating vector time with 758 elements.
Creating vector flow with 758 elements.
Creating vector time with 758 elements.
Creating vector humidity with 758 elements.
Creating vector time with 758 elements.
Creating vector temperature with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_0 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_1 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_2 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_3 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_4 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_5 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_6 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_7 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_8 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_9 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_10 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_11 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_12 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_13 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_14 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_15 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_16 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_17 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_18 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_19 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_20 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_21 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_22 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_23 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_24 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_25 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_26 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_27 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_28 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_29 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_30 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_31 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_32 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_33 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_34 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_35 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_36 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_37 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_38 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_39 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_40 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_41 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_42 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_43 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_44 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_45 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_46 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_47 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_48 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_49 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_50 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_51 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_52 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_53 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_54 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_55 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_56 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_57 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_58 with 758 elements.
Creating vector time with 758 elements.
Creating vector raw_59 with 758 elements.
Creating vector time with 758 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.01/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/2005/2005332/2005.332.01/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/2005/2005332/2005.332.01/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/2005/2005332/2005.332.01/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/2005/2005332/2005.332.01/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_2005.332.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2005.332.02
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/
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/2005/2005332/2005.332.02/navigation.nc')
Creating vector time with 7029 elements.
Creating vector mPos_x with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mPos_y with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mDepth with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mGpsNorth with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mGpsEast with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mGpsValid with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mPhi with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mTheta with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mPsi with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mOmega_x with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mOmega_y with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mOmega_z with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mPsaRange with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mAltitude with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mDvlAltitude with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mWaterSpeed with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mDvlValid with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mDvlNewData with 7029 elements.
Creating vector time with 7029 elements.
Creating vector mDeltaT with 7029 elements.
Creating vector time with 7029 elements.
Creating vector nfix with 7029 elements.
Creating vector time with 7029 elements.
Creating vector efix with 7029 elements.
Creating vector time with 7029 elements.
Creating vector filter_north with 7029 elements.
Creating vector time with 7029 elements.
Creating vector filter_east with 7029 elements.
Creating vector time with 7029 elements.
Creating vector filter_depth with 7029 elements.
Creating vector time with 7029 elements.
Creating vector north_current with 7029 elements.
Creating vector time with 7029 elements.
Creating vector east_current with 7029 elements.
Creating vector time with 7029 elements.
Creating vector speed_bias with 7029 elements.
Creating vector time with 7029 elements.
Creating vector heading_bias with 7029 elements.
Creating vector time with 7029 elements.
Creating vector latitude with 7029 elements.
Creating vector time with 7029 elements.
Creating vector longitude with 7029 elements.
Creating vector time with 7029 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/navigation.nc');
processNav(): median of positive valued depths = 24.1076
processNav(): Finding depths less than 168.7535 and times > 0
processNav(): length(Nav.depth) = 7029
processNav(): length(gindx)     = 7029
 
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/2005/2005332/2005.332.02/gps.nc')
Creating vector time with 108 elements.
Creating vector hours with 108 elements.
Creating vector time with 108 elements.
Creating vector minutes with 108 elements.
Creating vector time with 108 elements.
Creating vector seconds with 108 elements.
Creating vector time with 108 elements.
Creating vector centiSeconds with 108 elements.
Creating vector time with 108 elements.
Creating vector latitude with 108 elements.
Creating vector time with 108 elements.
Creating vector longitude with 108 elements.
Creating vector time with 108 elements.
Creating vector quality with 108 elements.
Creating vector time with 108 elements.
Creating vector numberOfSatellites with 108 elements.
Creating vector time with 108 elements.
Creating vector hdop with 108 elements.
Creating vector time with 108 elements.
Creating vector antennaHeight with 108 elements.
Creating vector time with 108 elements.
Creating vector geoHeight with 108 elements.
Creating vector time with 108 elements.
Creating vector dgpsDataAge with 108 elements.
Creating vector time with 108 elements.
Creating vector dgpsRSID with 108 elements.
Creating vector time with 108 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/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/2005/2005332/2005.332.02/parosci.nc')
Creating vector time with 15243 elements.
Creating vector depth with 15243 elements.
Creating vector time with 15243 elements.
Creating vector temp with 15243 elements.
Creating vector time with 15243 elements.
Creating vector pressure with 15243 elements.
Creating vector time with 15243 elements.
Creating vector temp_period with 15243 elements.
Creating vector time with 15243 elements.
Creating vector pres_period with 15243 elements.
Creating vector time with 15243 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.31481 max(Depth.data) = 53.8191
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.31481 max(Depth.data) = 53.8191
 
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/2005/2005332/2005.332.02/hydroscatlog.nc')
Creating vector time with 5684 elements.
Creating vector Seconds with 5684 elements.
Creating vector time with 5684 elements.
Creating vector HundrethsOfSeconds with 5684 elements.
Creating vector time with 5684 elements.
Creating vector Snorm1 with 5684 elements.
Creating vector time with 5684 elements.
Creating vector Snorm2 with 5684 elements.
Creating vector time with 5684 elements.
Creating vector Snorm3 with 5684 elements.
Creating vector time with 5684 elements.
Creating vector Gain_Status_1 with 5684 elements.
Creating vector time with 5684 elements.
Creating vector Gain_Status_2 with 5684 elements.
Creating vector time with 5684 elements.
Creating vector Gain_Status_3 with 5684 elements.
Creating vector time with 5684 elements.
Creating vector RawDepthValue with 5684 elements.
Creating vector time with 5684 elements.
Creating vector RawTempValue with 5684 elements.
Creating vector time with 5684 elements.
Creating vector Temperature with 5684 elements.
Creating vector time with 5684 elements.
Creating vector ErrorValue with 5684 elements.
Creating vector time with 5684 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/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/2005/2005332/2005.332.02/ctdDriver.nc')
Creating vector time with 5590 elements.
Creating vector conductivity with 5590 elements.
Creating vector time with 5590 elements.
Creating vector temperature with 5590 elements.
Creating vector time with 5590 elements.
Creating vector cond_frequency with 5590 elements.
Creating vector time with 5590 elements.
Creating vector temp_frequency with 5590 elements.
Creating vector time with 5590 elements.
Creating vector spare with 5590 elements.
Creating vector time with 5590 elements.
Creating vector humidity with 5590 elements.
Creating vector time with 5590 elements.
Creating vector flow1 with 5590 elements.
Creating vector time with 5590 elements.
Creating vector OBS with 5590 elements.
Creating vector time with 5590 elements.
Creating vector dissolvedO2 with 5590 elements.
Creating vector time with 5590 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/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/2005/2005332/2005.332.02/ctdDriver2.nc')
Creating vector time with 5589 elements.
Creating vector conductivity with 5589 elements.
Creating vector time with 5589 elements.
Creating vector temperature with 5589 elements.
Creating vector time with 5589 elements.
Creating vector cond_frequency with 5589 elements.
Creating vector time with 5589 elements.
Creating vector temp_frequency with 5589 elements.
Creating vector time with 5589 elements.
Creating vector flow2 with 5589 elements.
Creating vector time with 5589 elements.
Creating vector spare with 5589 elements.
Creating vector time with 5589 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/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/2005/2005332/2005.332.02/isuslog.nc')
Creating vector time with 848 elements.
Creating vector isusNitrate with 848 elements.
Creating vector time with 848 elements.
Creating vector isusTemp with 848 elements.
Creating vector time with 848 elements.
Creating vector isusQuality with 848 elements.
Creating vector time with 848 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/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/2005/2005332/2005.332.02/biolume.nc')
Creating vector time with 1426 elements.
Creating vector rrr with 1426 elements.
Creating vector time with 1426 elements.
Creating vector cal_striing with 1426 elements.
Creating vector time with 1426 elements.
Creating vector pump with 1426 elements.
Creating vector time with 1426 elements.
Creating vector flow with 1426 elements.
Creating vector time with 1426 elements.
Creating vector humidity with 1426 elements.
Creating vector time with 1426 elements.
Creating vector temperature with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_0 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_1 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_2 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_3 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_4 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_5 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_6 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_7 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_8 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_9 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_10 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_11 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_12 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_13 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_14 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_15 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_16 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_17 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_18 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_19 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_20 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_21 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_22 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_23 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_24 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_25 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_26 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_27 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_28 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_29 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_30 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_31 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_32 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_33 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_34 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_35 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_36 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_37 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_38 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_39 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_40 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_41 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_42 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_43 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_44 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_45 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_46 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_47 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_48 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_49 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_50 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_51 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_52 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_53 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_54 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_55 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_56 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_57 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_58 with 1426 elements.
Creating vector time with 1426 elements.
Creating vector raw_59 with 1426 elements.
Creating vector time with 1426 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.02/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/2005/2005332/2005.332.02/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/2005/2005332/2005.332.02/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/2005/2005332/2005.332.02/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/2005/2005332/2005.332.02/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_2005.332.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2005.332.03
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/
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/2005/2005332/2005.332.03/navigation.nc')
Creating vector time with 8617 elements.
Creating vector mPos_x with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mPos_y with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mDepth with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mGpsNorth with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mGpsEast with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mGpsValid with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mPhi with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mTheta with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mPsi with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mOmega_x with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mOmega_y with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mOmega_z with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mPsaRange with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mAltitude with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mDvlAltitude with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mWaterSpeed with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mDvlValid with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mDvlNewData with 8617 elements.
Creating vector time with 8617 elements.
Creating vector mDeltaT with 8617 elements.
Creating vector time with 8617 elements.
Creating vector nfix with 8617 elements.
Creating vector time with 8617 elements.
Creating vector efix with 8617 elements.
Creating vector time with 8617 elements.
Creating vector filter_north with 8617 elements.
Creating vector time with 8617 elements.
Creating vector filter_east with 8617 elements.
Creating vector time with 8617 elements.
Creating vector filter_depth with 8617 elements.
Creating vector time with 8617 elements.
Creating vector north_current with 8617 elements.
Creating vector time with 8617 elements.
Creating vector east_current with 8617 elements.
Creating vector time with 8617 elements.
Creating vector speed_bias with 8617 elements.
Creating vector time with 8617 elements.
Creating vector heading_bias with 8617 elements.
Creating vector time with 8617 elements.
Creating vector latitude with 8617 elements.
Creating vector time with 8617 elements.
Creating vector longitude with 8617 elements.
Creating vector time with 8617 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/navigation.nc');
processNav(): median of positive valued depths = 34.45
processNav(): Finding depths less than 241.1501 and times > 0
processNav(): length(Nav.depth) = 8617
processNav(): length(gindx)     = 8617
 
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/2005/2005332/2005.332.03/gps.nc')
Creating vector time with 127 elements.
Creating vector hours with 127 elements.
Creating vector time with 127 elements.
Creating vector minutes with 127 elements.
Creating vector time with 127 elements.
Creating vector seconds with 127 elements.
Creating vector time with 127 elements.
Creating vector centiSeconds with 127 elements.
Creating vector time with 127 elements.
Creating vector latitude with 127 elements.
Creating vector time with 127 elements.
Creating vector longitude with 127 elements.
Creating vector time with 127 elements.
Creating vector quality with 127 elements.
Creating vector time with 127 elements.
Creating vector numberOfSatellites with 127 elements.
Creating vector time with 127 elements.
Creating vector hdop with 127 elements.
Creating vector time with 127 elements.
Creating vector antennaHeight with 127 elements.
Creating vector time with 127 elements.
Creating vector geoHeight with 127 elements.
Creating vector time with 127 elements.
Creating vector dgpsDataAge with 127 elements.
Creating vector time with 127 elements.
Creating vector dgpsRSID with 127 elements.
Creating vector time with 127 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/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/2005/2005332/2005.332.03/parosci.nc')
Creating vector time with 18642 elements.
Creating vector depth with 18642 elements.
Creating vector time with 18642 elements.
Creating vector temp with 18642 elements.
Creating vector time with 18642 elements.
Creating vector pressure with 18642 elements.
Creating vector time with 18642 elements.
Creating vector temp_period with 18642 elements.
Creating vector time with 18642 elements.
Creating vector pres_period with 18642 elements.
Creating vector time with 18642 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.23118 max(Depth.data) = 47.4799
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.23118 max(Depth.data) = 47.4799
 
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/2005/2005332/2005.332.03/hydroscatlog.nc')
Creating vector time with 6951 elements.
Creating vector Seconds with 6951 elements.
Creating vector time with 6951 elements.
Creating vector HundrethsOfSeconds with 6951 elements.
Creating vector time with 6951 elements.
Creating vector Snorm1 with 6951 elements.
Creating vector time with 6951 elements.
Creating vector Snorm2 with 6951 elements.
Creating vector time with 6951 elements.
Creating vector Snorm3 with 6951 elements.
Creating vector time with 6951 elements.
Creating vector Gain_Status_1 with 6951 elements.
Creating vector time with 6951 elements.
Creating vector Gain_Status_2 with 6951 elements.
Creating vector time with 6951 elements.
Creating vector Gain_Status_3 with 6951 elements.
Creating vector time with 6951 elements.
Creating vector RawDepthValue with 6951 elements.
Creating vector time with 6951 elements.
Creating vector RawTempValue with 6951 elements.
Creating vector time with 6951 elements.
Creating vector Temperature with 6951 elements.
Creating vector time with 6951 elements.
Creating vector ErrorValue with 6951 elements.
Creating vector time with 6951 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/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/2005/2005332/2005.332.03/ctdDriver.nc')
Creating vector time with 6862 elements.
Creating vector conductivity with 6862 elements.
Creating vector time with 6862 elements.
Creating vector temperature with 6862 elements.
Creating vector time with 6862 elements.
Creating vector cond_frequency with 6862 elements.
Creating vector time with 6862 elements.
Creating vector temp_frequency with 6862 elements.
Creating vector time with 6862 elements.
Creating vector spare with 6862 elements.
Creating vector time with 6862 elements.
Creating vector humidity with 6862 elements.
Creating vector time with 6862 elements.
Creating vector flow1 with 6862 elements.
Creating vector time with 6862 elements.
Creating vector OBS with 6862 elements.
Creating vector time with 6862 elements.
Creating vector dissolvedO2 with 6862 elements.
Creating vector time with 6862 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/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/2005/2005332/2005.332.03/ctdDriver2.nc')
Creating vector time with 6862 elements.
Creating vector conductivity with 6862 elements.
Creating vector time with 6862 elements.
Creating vector temperature with 6862 elements.
Creating vector time with 6862 elements.
Creating vector cond_frequency with 6862 elements.
Creating vector time with 6862 elements.
Creating vector temp_frequency with 6862 elements.
Creating vector time with 6862 elements.
Creating vector flow2 with 6862 elements.
Creating vector time with 6862 elements.
Creating vector spare with 6862 elements.
Creating vector time with 6862 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/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/2005/2005332/2005.332.03/isuslog.nc')
Creating vector time with 1050 elements.
Creating vector isusNitrate with 1050 elements.
Creating vector time with 1050 elements.
Creating vector isusTemp with 1050 elements.
Creating vector time with 1050 elements.
Creating vector isusQuality with 1050 elements.
Creating vector time with 1050 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/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/2005/2005332/2005.332.03/biolume.nc')
Creating vector time with 1744 elements.
Creating vector rrr with 1744 elements.
Creating vector time with 1744 elements.
Creating vector cal_striing with 1744 elements.
Creating vector time with 1744 elements.
Creating vector pump with 1744 elements.
Creating vector time with 1744 elements.
Creating vector flow with 1744 elements.
Creating vector time with 1744 elements.
Creating vector humidity with 1744 elements.
Creating vector time with 1744 elements.
Creating vector temperature with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_0 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_1 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_2 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_3 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_4 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_5 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_6 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_7 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_8 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_9 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_10 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_11 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_12 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_13 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_14 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_15 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_16 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_17 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_18 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_19 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_20 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_21 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_22 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_23 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_24 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_25 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_26 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_27 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_28 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_29 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_30 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_31 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_32 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_33 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_34 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_35 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_36 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_37 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_38 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_39 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_40 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_41 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_42 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_43 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_44 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_45 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_46 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_47 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_48 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_49 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_50 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_51 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_52 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_53 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_54 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_55 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_56 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_57 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_58 with 1744 elements.
Creating vector time with 1744 elements.
Creating vector raw_59 with 1744 elements.
Creating vector time with 1744 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.03/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/2005/2005332/2005.332.03/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/2005/2005332/2005.332.03/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/2005/2005332/2005.332.03/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/2005/2005332/2005.332.03/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_2005.332.03.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2005.332.04
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/
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/2005/2005332/2005.332.04/navigation.nc')
Creating vector time with 38687 elements.
Creating vector mPos_x with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mPos_y with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mDepth with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mGpsNorth with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mGpsEast with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mGpsValid with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mPhi with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mTheta with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mPsi with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mOmega_x with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mOmega_y with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mOmega_z with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mPsaRange with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mAltitude with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mDvlAltitude with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mWaterSpeed with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mDvlValid with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mDvlNewData with 38687 elements.
Creating vector time with 38687 elements.
Creating vector mDeltaT with 38687 elements.
Creating vector time with 38687 elements.
Creating vector nfix with 38687 elements.
Creating vector time with 38687 elements.
Creating vector efix with 38687 elements.
Creating vector time with 38687 elements.
Creating vector filter_north with 38687 elements.
Creating vector time with 38687 elements.
Creating vector filter_east with 38687 elements.
Creating vector time with 38687 elements.
Creating vector filter_depth with 38687 elements.
Creating vector time with 38687 elements.
Creating vector north_current with 38687 elements.
Creating vector time with 38687 elements.
Creating vector east_current with 38687 elements.
Creating vector time with 38687 elements.
Creating vector speed_bias with 38687 elements.
Creating vector time with 38687 elements.
Creating vector heading_bias with 38687 elements.
Creating vector time with 38687 elements.
Creating vector latitude with 38687 elements.
Creating vector time with 38687 elements.
Creating vector longitude with 38687 elements.
Creating vector time with 38687 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/navigation.nc');
processNav(): median of positive valued depths = 28.1073
processNav(): Finding depths less than 196.7514 and times > 0
processNav(): length(Nav.depth) = 38687
processNav(): length(gindx)     = 38687
 
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/2005/2005332/2005.332.04/gps.nc')
Creating vector time with 264 elements.
Creating vector hours with 264 elements.
Creating vector time with 264 elements.
Creating vector minutes with 264 elements.
Creating vector time with 264 elements.
Creating vector seconds with 264 elements.
Creating vector time with 264 elements.
Creating vector centiSeconds with 264 elements.
Creating vector time with 264 elements.
Creating vector latitude with 264 elements.
Creating vector time with 264 elements.
Creating vector longitude with 264 elements.
Creating vector time with 264 elements.
Creating vector quality with 264 elements.
Creating vector time with 264 elements.
Creating vector numberOfSatellites with 264 elements.
Creating vector time with 264 elements.
Creating vector hdop with 264 elements.
Creating vector time with 264 elements.
Creating vector antennaHeight with 264 elements.
Creating vector time with 264 elements.
Creating vector geoHeight with 264 elements.
Creating vector time with 264 elements.
Creating vector dgpsDataAge with 264 elements.
Creating vector time with 264 elements.
Creating vector dgpsRSID with 264 elements.
Creating vector time with 264 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/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/2005/2005332/2005.332.04/parosci.nc')
Creating vector time with 82950 elements.
Creating vector depth with 82950 elements.
Creating vector time with 82950 elements.
Creating vector temp with 82950 elements.
Creating vector time with 82950 elements.
Creating vector pressure with 82950 elements.
Creating vector time with 82950 elements.
Creating vector temp_period with 82950 elements.
Creating vector time with 82950 elements.
Creating vector pres_period with 82950 elements.
Creating vector time with 82950 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.15943 max(Depth.data) = 48.1938
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.15943 max(Depth.data) = 48.1938
 
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/2005/2005332/2005.332.04/hydroscatlog.nc')
Creating vector time with 31009 elements.
Creating vector Seconds with 31009 elements.
Creating vector time with 31009 elements.
Creating vector HundrethsOfSeconds with 31009 elements.
Creating vector time with 31009 elements.
Creating vector Snorm1 with 31009 elements.
Creating vector time with 31009 elements.
Creating vector Snorm2 with 31009 elements.
Creating vector time with 31009 elements.
Creating vector Snorm3 with 31009 elements.
Creating vector time with 31009 elements.
Creating vector Gain_Status_1 with 31009 elements.
Creating vector time with 31009 elements.
Creating vector Gain_Status_2 with 31009 elements.
Creating vector time with 31009 elements.
Creating vector Gain_Status_3 with 31009 elements.
Creating vector time with 31009 elements.
Creating vector RawDepthValue with 31009 elements.
Creating vector time with 31009 elements.
Creating vector RawTempValue with 31009 elements.
Creating vector time with 31009 elements.
Creating vector Temperature with 31009 elements.
Creating vector time with 31009 elements.
Creating vector ErrorValue with 31009 elements.
Creating vector time with 31009 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/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/2005/2005332/2005.332.04/ctdDriver.nc')
Creating vector time with 30925 elements.
Creating vector conductivity with 30925 elements.
Creating vector time with 30925 elements.
Creating vector temperature with 30925 elements.
Creating vector time with 30925 elements.
Creating vector cond_frequency with 30925 elements.
Creating vector time with 30925 elements.
Creating vector temp_frequency with 30925 elements.
Creating vector time with 30925 elements.
Creating vector spare with 30925 elements.
Creating vector time with 30925 elements.
Creating vector humidity with 30925 elements.
Creating vector time with 30925 elements.
Creating vector flow1 with 30925 elements.
Creating vector time with 30925 elements.
Creating vector OBS with 30925 elements.
Creating vector time with 30925 elements.
Creating vector dissolvedO2 with 30925 elements.
Creating vector time with 30925 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/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/2005/2005332/2005.332.04/ctdDriver2.nc')
Creating vector time with 30925 elements.
Creating vector conductivity with 30925 elements.
Creating vector time with 30925 elements.
Creating vector temperature with 30925 elements.
Creating vector time with 30925 elements.
Creating vector cond_frequency with 30925 elements.
Creating vector time with 30925 elements.
Creating vector temp_frequency with 30925 elements.
Creating vector time with 30925 elements.
Creating vector flow2 with 30925 elements.
Creating vector time with 30925 elements.
Creating vector spare with 30925 elements.
Creating vector time with 30925 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/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/2005/2005332/2005.332.04/isuslog.nc')
Creating vector time with 4862 elements.
Creating vector isusNitrate with 4862 elements.
Creating vector time with 4862 elements.
Creating vector isusTemp with 4862 elements.
Creating vector time with 4862 elements.
Creating vector isusQuality with 4862 elements.
Creating vector time with 4862 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/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/2005/2005332/2005.332.04/biolume.nc')
Creating vector time with 7762 elements.
Creating vector rrr with 7762 elements.
Creating vector time with 7762 elements.
Creating vector cal_striing with 7762 elements.
Creating vector time with 7762 elements.
Creating vector pump with 7762 elements.
Creating vector time with 7762 elements.
Creating vector flow with 7762 elements.
Creating vector time with 7762 elements.
Creating vector humidity with 7762 elements.
Creating vector time with 7762 elements.
Creating vector temperature with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_0 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_1 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_2 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_3 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_4 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_5 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_6 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_7 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_8 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_9 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_10 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_11 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_12 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_13 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_14 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_15 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_16 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_17 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_18 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_19 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_20 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_21 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_22 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_23 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_24 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_25 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_26 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_27 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_28 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_29 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_30 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_31 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_32 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_33 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_34 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_35 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_36 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_37 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_38 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_39 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_40 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_41 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_42 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_43 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_44 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_45 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_46 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_47 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_48 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_49 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_50 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_51 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_52 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_53 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_54 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_55 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_56 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_57 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_58 with 7762 elements.
Creating vector time with 7762 elements.
Creating vector raw_59 with 7762 elements.
Creating vector time with 7762 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005332/2005.332.04/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/2005/2005332/2005.332.04/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/2005/2005332/2005.332.04/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/2005/2005332/2005.332.04/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/2005/2005332/2005.332.04/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_2005.332.04.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_2005.332.00.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.332.01.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.332.02.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.332.03.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.332.04.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 8 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_332_00_332_04_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_332_00_332_04.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_332_00_332_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 = 104 Gridding with nix = 312, iZ = 105
Using mean boxcar filter of vector...
Using mean boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Gridding...
   T
   S
   O
Using median boxcar filter of vector...
Using median boxcar filter of vector...
Using median boxcar filter of vector...
   bbp470
   bbp676
   fl676_uncorr
   N
   BL
   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 61869 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 61869 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 119063 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 11/28/2005 07:30  to 11/28/2005 14:30 

swr =

   26.4276
  108.1499
  292.8908
  372.3385
  406.1303
  409.5836
  370.3264
  293.7487

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_332_00_332_04_swr.png
[Warning: Contour not rendered for constant ZData] 
[> In contourf (line 60)
  In plot_sections (line 564)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
Done plotting SWR.
Executing: /bin/rm -f ../results/2005332_GulperTimes.txt && touch ../results/2005332_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/2005/2005332/2005.332.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005332/2005.332.00/syslog -startEsecs 1133209963.1625 -surveyName Dorado389_2005_332_00_332_04 >> ../results/2005332_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005332_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/2005/2005332/2005.332.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005332/2005.332.01/syslog -startEsecs 1133209963.1625 -surveyName Dorado389_2005_332_00_332_04 >> ../results/2005332_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005332_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/2005/2005332/2005.332.02/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005332/2005.332.02/syslog -startEsecs 1133209963.1625 -surveyName Dorado389_2005_332_00_332_04 >> ../results/2005332_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005332_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/2005/2005332/2005.332.03/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005332/2005.332.03/syslog -startEsecs 1133209963.1625 -surveyName Dorado389_2005_332_00_332_04 >> ../results/2005332_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005332_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/2005/2005332/2005.332.04/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005332/2005.332.04/syslog -startEsecs 1133209963.1625 -surveyName Dorado389_2005_332_00_332_04 >> ../results/2005332_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005332_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_332_00_332_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_332_00_332_04_2column.png
Elapsed time to save image: 7 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_332_00_332_04_biolume.png
Elapsed time to save image: 30 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_332_00_332_04_lopc.png
Elapsed time to save image: 7 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_332_00_332_04_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_332_00_332_04_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_332_00_332_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_332_00_332_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_332_00_332_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_332_00_332_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_332_00_332_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_332_00_332_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_332_00_332_04_Temperature.kml (deflated 95%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_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_332_00_332_04_Salinity.kml (deflated 95%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_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);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_04_Nitrate.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_04_Nitrate.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, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_04_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_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);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_04_Optical_Backscatter_470_nm.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_04_Optical_Backscatter_470_nm.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 @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_04_Optical_Backscatter_676_nm.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_04_Optical_Backscatter_676_nm.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, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_04_Chlorophyll_Fluorescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_04_Chlorophyll_Fluorescence.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, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_04_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_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_332_00_332_04_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_332_00_332_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_332_00_332_04.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_332_00_332_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_332_00_332_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_332_00_332_04.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
1 NaNs found in bbpRed.  Interpolating anyway.
Encountered 29 NaN values in array of lon that is 7657 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 7628 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 7628 are not equal to number of Lat lon points = 7657
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_332_00_332_04.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_332_00_332_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_332_00_332_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_332_00_332_04_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
1 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_332_00_332_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_332_00_332_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_332_00_332_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_332_00_332_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_332_00_332_04 processed" mccann@mbari.org < mail_Dorado389_2005_332_00_332_04.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.332.00.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.332.01.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.332.02.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.332.03.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.332.04.mat
Processing time: 145 seconds