Execution of AUVprocess_main version 1.86 at 2018-05-31T02:16:33Z on elvis
Matlab command executed: 
   AUVprocess_main('BIOLUME', 2005, ['182.00';'182.01';'182.02'], '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: 2005.182.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.00/
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/2005/2005182/2005.182.00/navigation.nc')
Creating vector time with 2509 elements.
Creating vector mPos_x with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mPos_y with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mDepth with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mGpsNorth with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mGpsEast with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mGpsValid with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mPhi with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mTheta with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mPsi with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mOmega_x with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mOmega_y with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mOmega_z with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mPsaRange with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mAltitude with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mDvlAltitude with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mWaterSpeed with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mDvlValid with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mDvlNewData with 2509 elements.
Creating vector time with 2509 elements.
Creating vector mDeltaT with 2509 elements.
Creating vector time with 2509 elements.
Creating vector nfix with 2509 elements.
Creating vector time with 2509 elements.
Creating vector efix with 2509 elements.
Creating vector time with 2509 elements.
Creating vector filter_north with 2509 elements.
Creating vector time with 2509 elements.
Creating vector filter_east with 2509 elements.
Creating vector time with 2509 elements.
Creating vector filter_depth with 2509 elements.
Creating vector time with 2509 elements.
Creating vector north_current with 2509 elements.
Creating vector time with 2509 elements.
Creating vector east_current with 2509 elements.
Creating vector time with 2509 elements.
Creating vector speed_bias with 2509 elements.
Creating vector time with 2509 elements.
Creating vector heading_bias with 2509 elements.
Creating vector time with 2509 elements.
Creating vector latitude with 2509 elements.
Creating vector time with 2509 elements.
Creating vector longitude with 2509 elements.
Creating vector time with 2509 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.00/navigation.nc');
processNav(): median of positive valued depths = 4.9253
processNav(): Finding depths less than 34.4768 and times > 0
processNav(): length(Nav.depth) = 2509
processNav(): length(gindx)     = 2509
 
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/2005/2005182/2005.182.00/gps.nc')
Creating vector time with 204 elements.
Creating vector hours with 204 elements.
Creating vector time with 204 elements.
Creating vector minutes with 204 elements.
Creating vector time with 204 elements.
Creating vector seconds with 204 elements.
Creating vector time with 204 elements.
Creating vector centiSeconds with 204 elements.
Creating vector time with 204 elements.
Creating vector latitude with 204 elements.
Creating vector time with 204 elements.
Creating vector longitude with 204 elements.
Creating vector time with 204 elements.
Creating vector quality with 204 elements.
Creating vector time with 204 elements.
Creating vector numberOfSatellites with 204 elements.
Creating vector time with 204 elements.
Creating vector hdop with 204 elements.
Creating vector time with 204 elements.
Creating vector antennaHeight with 204 elements.
Creating vector time with 204 elements.
Creating vector geoHeight with 204 elements.
Creating vector time with 204 elements.
Creating vector dgpsDataAge with 204 elements.
Creating vector time with 204 elements.
Creating vector dgpsRSID with 204 elements.
Creating vector time with 204 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.00/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/2005/2005182/2005.182.00/parosci.nc')
Creating vector time with 5590 elements.
Creating vector depth with 5590 elements.
Creating vector time with 5590 elements.
Creating vector temp with 5590 elements.
Creating vector time with 5590 elements.
Creating vector pressure with 5590 elements.
Creating vector time with 5590 elements.
Creating vector temp_period with 5590 elements.
Creating vector time with 5590 elements.
Creating vector pres_period 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/2005/2005182/2005.182.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.20381 max(Depth.data) = 11.5794
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.20381 max(Depth.data) = 11.5794
 
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/2005/2005182/2005.182.00/hydroscatlog.nc')
Creating vector time with 2075 elements.
Creating vector Seconds with 2075 elements.
Creating vector time with 2075 elements.
Creating vector HundrethsOfSeconds with 2075 elements.
Creating vector time with 2075 elements.
Creating vector Snorm1 with 2075 elements.
Creating vector time with 2075 elements.
Creating vector Snorm2 with 2075 elements.
Creating vector time with 2075 elements.
Creating vector Snorm3 with 2075 elements.
Creating vector time with 2075 elements.
Creating vector Gain_Status_1 with 2075 elements.
Creating vector time with 2075 elements.
Creating vector Gain_Status_2 with 2075 elements.
Creating vector time with 2075 elements.
Creating vector Gain_Status_3 with 2075 elements.
Creating vector time with 2075 elements.
Creating vector RawDepthValue with 2075 elements.
Creating vector time with 2075 elements.
Creating vector RawTempValue with 2075 elements.
Creating vector time with 2075 elements.
Creating vector Temperature with 2075 elements.
Creating vector time with 2075 elements.
Creating vector ErrorValue with 2075 elements.
Creating vector time with 2075 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.00/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/2005/2005182/2005.182.00/ctdDriver.nc')
Creating vector time with 1984 elements.
Creating vector conductivity with 1984 elements.
Creating vector time with 1984 elements.
Creating vector temperature with 1984 elements.
Creating vector time with 1984 elements.
Creating vector cond_frequency with 1984 elements.
Creating vector time with 1984 elements.
Creating vector temp_frequency with 1984 elements.
Creating vector time with 1984 elements.
Creating vector spare with 1984 elements.
Creating vector time with 1984 elements.
Creating vector humidity with 1984 elements.
Creating vector time with 1984 elements.
Creating vector flow1 with 1984 elements.
Creating vector time with 1984 elements.
Creating vector OBS with 1984 elements.
Creating vector time with 1984 elements.
Creating vector dissolvedO2 with 1984 elements.
Creating vector time with 1984 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.00/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/2005/2005182/2005.182.00/ctdDriver2.nc')
Creating vector time with 1985 elements.
Creating vector conductivity with 1985 elements.
Creating vector time with 1985 elements.
Creating vector temperature with 1985 elements.
Creating vector time with 1985 elements.
Creating vector cond_frequency with 1985 elements.
Creating vector time with 1985 elements.
Creating vector temp_frequency with 1985 elements.
Creating vector time with 1985 elements.
Creating vector flow2 with 1985 elements.
Creating vector time with 1985 elements.
Creating vector spare with 1985 elements.
Creating vector time with 1985 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.00/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/2005/2005182/2005.182.00/isuslog.nc')
Creating vector time with 292 elements.
Creating vector isusNitrate with 292 elements.
Creating vector time with 292 elements.
Creating vector isusTemp with 292 elements.
Creating vector time with 292 elements.
Creating vector isusQuality with 292 elements.
Creating vector time with 292 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.00/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/2005/2005182/2005.182.00/biolume.nc')
Creating vector time with 524 elements.
Creating vector rrr with 524 elements.
Creating vector time with 524 elements.
Creating vector cal_striing with 524 elements.
Creating vector time with 524 elements.
Creating vector pump with 524 elements.
Creating vector time with 524 elements.
Creating vector flow with 524 elements.
Creating vector time with 524 elements.
Creating vector humidity with 524 elements.
Creating vector time with 524 elements.
Creating vector temperature with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_0 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_1 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_2 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_3 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_4 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_5 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_6 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_7 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_8 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_9 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_10 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_11 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_12 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_13 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_14 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_15 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_16 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_17 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_18 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_19 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_20 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_21 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_22 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_23 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_24 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_25 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_26 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_27 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_28 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_29 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_30 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_31 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_32 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_33 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_34 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_35 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_36 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_37 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_38 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_39 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_40 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_41 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_42 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_43 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_44 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_45 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_46 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_47 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_48 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_49 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_50 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_51 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_52 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_53 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_54 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_55 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_56 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_57 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_58 with 524 elements.
Creating vector time with 524 elements.
Creating vector raw_59 with 524 elements.
Creating vector time with 524 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.00/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/2005/2005182/2005.182.00/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/2005/2005182/2005.182.00/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/2005/2005182/2005.182.00/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/2005/2005182/2005.182.00/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_2005.182.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
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Processing AUV mission: 2005.182.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/
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/2005/2005182/2005.182.01/navigation.nc')
Creating vector time with 94018 elements.
Creating vector mPos_x with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mPos_y with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mDepth with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mGpsNorth with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mGpsEast with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mGpsValid with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mPhi with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mTheta with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mPsi with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mOmega_x with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mOmega_y with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mOmega_z with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mPsaRange with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mAltitude with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mDvlAltitude with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mWaterSpeed with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mDvlValid with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mDvlNewData with 94018 elements.
Creating vector time with 94018 elements.
Creating vector mDeltaT with 94018 elements.
Creating vector time with 94018 elements.
Creating vector nfix with 94018 elements.
Creating vector time with 94018 elements.
Creating vector efix with 94018 elements.
Creating vector time with 94018 elements.
Creating vector filter_north with 94018 elements.
Creating vector time with 94018 elements.
Creating vector filter_east with 94018 elements.
Creating vector time with 94018 elements.
Creating vector filter_depth with 94018 elements.
Creating vector time with 94018 elements.
Creating vector north_current with 94018 elements.
Creating vector time with 94018 elements.
Creating vector east_current with 94018 elements.
Creating vector time with 94018 elements.
Creating vector speed_bias with 94018 elements.
Creating vector time with 94018 elements.
Creating vector heading_bias with 94018 elements.
Creating vector time with 94018 elements.
Creating vector latitude with 94018 elements.
Creating vector time with 94018 elements.
Creating vector longitude with 94018 elements.
Creating vector time with 94018 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/navigation.nc');
processNav(): median of positive valued depths = 35.0924
processNav(): Finding depths less than 245.6467 and times > 0
processNav(): length(Nav.depth) = 94018
processNav(): length(gindx)     = 94018
 
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/2005/2005182/2005.182.01/gps.nc')
Creating vector time with 746 elements.
Creating vector hours with 746 elements.
Creating vector time with 746 elements.
Creating vector minutes with 746 elements.
Creating vector time with 746 elements.
Creating vector seconds with 746 elements.
Creating vector time with 746 elements.
Creating vector centiSeconds with 746 elements.
Creating vector time with 746 elements.
Creating vector latitude with 746 elements.
Creating vector time with 746 elements.
Creating vector longitude with 746 elements.
Creating vector time with 746 elements.
Creating vector quality with 746 elements.
Creating vector time with 746 elements.
Creating vector numberOfSatellites with 746 elements.
Creating vector time with 746 elements.
Creating vector hdop with 746 elements.
Creating vector time with 746 elements.
Creating vector antennaHeight with 746 elements.
Creating vector time with 746 elements.
Creating vector geoHeight with 746 elements.
Creating vector time with 746 elements.
Creating vector dgpsDataAge with 746 elements.
Creating vector time with 746 elements.
Creating vector dgpsRSID with 746 elements.
Creating vector time with 746 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/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/2005/2005182/2005.182.01/parosci.nc')
Creating vector time with 201375 elements.
Creating vector depth with 201375 elements.
Creating vector time with 201375 elements.
Creating vector temp with 201375 elements.
Creating vector time with 201375 elements.
Creating vector pressure with 201375 elements.
Creating vector time with 201375 elements.
Creating vector temp_period with 201375 elements.
Creating vector time with 201375 elements.
Creating vector pres_period with 201375 elements.
Creating vector time with 201375 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.18508 max(Depth.data) = 99.4864
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.18508 max(Depth.data) = 99.4864
 
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/2005/2005182/2005.182.01/hydroscatlog.nc')
Creating vector time with 75251 elements.
Creating vector Seconds with 75251 elements.
Creating vector time with 75251 elements.
Creating vector HundrethsOfSeconds with 75251 elements.
Creating vector time with 75251 elements.
Creating vector Snorm1 with 75251 elements.
Creating vector time with 75251 elements.
Creating vector Snorm2 with 75251 elements.
Creating vector time with 75251 elements.
Creating vector Snorm3 with 75251 elements.
Creating vector time with 75251 elements.
Creating vector Gain_Status_1 with 75251 elements.
Creating vector time with 75251 elements.
Creating vector Gain_Status_2 with 75251 elements.
Creating vector time with 75251 elements.
Creating vector Gain_Status_3 with 75251 elements.
Creating vector time with 75251 elements.
Creating vector RawDepthValue with 75251 elements.
Creating vector time with 75251 elements.
Creating vector RawTempValue with 75251 elements.
Creating vector time with 75251 elements.
Creating vector Temperature with 75251 elements.
Creating vector time with 75251 elements.
Creating vector ErrorValue with 75251 elements.
Creating vector time with 75251 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/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/2005/2005182/2005.182.01/ctdDriver.nc')
Creating vector time with 75193 elements.
Creating vector conductivity with 75193 elements.
Creating vector time with 75193 elements.
Creating vector temperature with 75193 elements.
Creating vector time with 75193 elements.
Creating vector cond_frequency with 75193 elements.
Creating vector time with 75193 elements.
Creating vector temp_frequency with 75193 elements.
Creating vector time with 75193 elements.
Creating vector spare with 75193 elements.
Creating vector time with 75193 elements.
Creating vector humidity with 75193 elements.
Creating vector time with 75193 elements.
Creating vector flow1 with 75193 elements.
Creating vector time with 75193 elements.
Creating vector OBS with 75193 elements.
Creating vector time with 75193 elements.
Creating vector dissolvedO2 with 75193 elements.
Creating vector time with 75193 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/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/2005/2005182/2005.182.01/ctdDriver2.nc')
Creating vector time with 75193 elements.
Creating vector conductivity with 75193 elements.
Creating vector time with 75193 elements.
Creating vector temperature with 75193 elements.
Creating vector time with 75193 elements.
Creating vector cond_frequency with 75193 elements.
Creating vector time with 75193 elements.
Creating vector temp_frequency with 75193 elements.
Creating vector time with 75193 elements.
Creating vector flow2 with 75193 elements.
Creating vector time with 75193 elements.
Creating vector spare with 75193 elements.
Creating vector time with 75193 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/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/2005/2005182/2005.182.01/isuslog.nc')
Creating vector time with 12621 elements.
Creating vector isusNitrate with 12621 elements.
Creating vector time with 12621 elements.
Creating vector isusTemp with 12621 elements.
Creating vector time with 12621 elements.
Creating vector isusQuality with 12621 elements.
Creating vector time with 12621 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/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/2005/2005182/2005.182.01/biolume.nc')
Creating vector time with 18828 elements.
Creating vector rrr with 18828 elements.
Creating vector time with 18828 elements.
Creating vector cal_striing with 18828 elements.
Creating vector time with 18828 elements.
Creating vector pump with 18828 elements.
Creating vector time with 18828 elements.
Creating vector flow with 18828 elements.
Creating vector time with 18828 elements.
Creating vector humidity with 18828 elements.
Creating vector time with 18828 elements.
Creating vector temperature with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_0 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_1 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_2 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_3 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_4 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_5 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_6 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_7 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_8 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_9 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_10 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_11 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_12 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_13 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_14 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_15 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_16 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_17 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_18 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_19 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_20 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_21 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_22 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_23 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_24 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_25 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_26 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_27 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_28 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_29 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_30 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_31 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_32 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_33 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_34 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_35 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_36 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_37 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_38 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_39 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_40 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_41 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_42 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_43 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_44 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_45 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_46 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_47 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_48 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_49 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_50 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_51 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_52 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_53 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_54 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_55 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_56 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_57 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_58 with 18828 elements.
Creating vector time with 18828 elements.
Creating vector raw_59 with 18828 elements.
Creating vector time with 18828 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.01/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/2005/2005182/2005.182.01/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/2005/2005182/2005.182.01/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/2005/2005182/2005.182.01/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/2005/2005182/2005.182.01/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_2005.182.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2005.182.02
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/
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/2005/2005182/2005.182.02/navigation.nc')
Creating vector time with 34599 elements.
Creating vector mPos_x with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mPos_y with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mDepth with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mGpsNorth with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mGpsEast with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mGpsValid with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mPhi with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mTheta with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mPsi with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mOmega_x with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mOmega_y with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mOmega_z with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mPsaRange with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mAltitude with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mDvlAltitude with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mWaterSpeed with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mDvlValid with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mDvlNewData with 34599 elements.
Creating vector time with 34599 elements.
Creating vector mDeltaT with 34599 elements.
Creating vector time with 34599 elements.
Creating vector nfix with 34599 elements.
Creating vector time with 34599 elements.
Creating vector efix with 34599 elements.
Creating vector time with 34599 elements.
Creating vector filter_north with 34599 elements.
Creating vector time with 34599 elements.
Creating vector filter_east with 34599 elements.
Creating vector time with 34599 elements.
Creating vector filter_depth with 34599 elements.
Creating vector time with 34599 elements.
Creating vector north_current with 34599 elements.
Creating vector time with 34599 elements.
Creating vector east_current with 34599 elements.
Creating vector time with 34599 elements.
Creating vector speed_bias with 34599 elements.
Creating vector time with 34599 elements.
Creating vector heading_bias with 34599 elements.
Creating vector time with 34599 elements.
Creating vector latitude with 34599 elements.
Creating vector time with 34599 elements.
Creating vector longitude with 34599 elements.
Creating vector time with 34599 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/navigation.nc');
processNav(): median of positive valued depths = 34.8777
processNav(): Finding depths less than 244.1439 and times > 0
processNav(): length(Nav.depth) = 34599
processNav(): length(gindx)     = 34599
 
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/2005/2005182/2005.182.02/gps.nc')
Creating vector time with 366 elements.
Creating vector hours with 366 elements.
Creating vector time with 366 elements.
Creating vector minutes with 366 elements.
Creating vector time with 366 elements.
Creating vector seconds with 366 elements.
Creating vector time with 366 elements.
Creating vector centiSeconds with 366 elements.
Creating vector time with 366 elements.
Creating vector latitude with 366 elements.
Creating vector time with 366 elements.
Creating vector longitude with 366 elements.
Creating vector time with 366 elements.
Creating vector quality with 366 elements.
Creating vector time with 366 elements.
Creating vector numberOfSatellites with 366 elements.
Creating vector time with 366 elements.
Creating vector hdop with 366 elements.
Creating vector time with 366 elements.
Creating vector antennaHeight with 366 elements.
Creating vector time with 366 elements.
Creating vector geoHeight with 366 elements.
Creating vector time with 366 elements.
Creating vector dgpsDataAge with 366 elements.
Creating vector time with 366 elements.
Creating vector dgpsRSID with 366 elements.
Creating vector time with 366 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/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/2005/2005182/2005.182.02/parosci.nc')
Creating vector time with 74236 elements.
Creating vector depth with 74236 elements.
Creating vector time with 74236 elements.
Creating vector temp with 74236 elements.
Creating vector time with 74236 elements.
Creating vector pressure with 74236 elements.
Creating vector time with 74236 elements.
Creating vector temp_period with 74236 elements.
Creating vector time with 74236 elements.
Creating vector pres_period with 74236 elements.
Creating vector time with 74236 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.20732 max(Depth.data) = 95.7587
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.20732 max(Depth.data) = 95.7587
 
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/2005/2005182/2005.182.02/hydroscatlog.nc')
Creating vector time with 27729 elements.
Creating vector Seconds with 27729 elements.
Creating vector time with 27729 elements.
Creating vector HundrethsOfSeconds with 27729 elements.
Creating vector time with 27729 elements.
Creating vector Snorm1 with 27729 elements.
Creating vector time with 27729 elements.
Creating vector Snorm2 with 27729 elements.
Creating vector time with 27729 elements.
Creating vector Snorm3 with 27729 elements.
Creating vector time with 27729 elements.
Creating vector Gain_Status_1 with 27729 elements.
Creating vector time with 27729 elements.
Creating vector Gain_Status_2 with 27729 elements.
Creating vector time with 27729 elements.
Creating vector Gain_Status_3 with 27729 elements.
Creating vector time with 27729 elements.
Creating vector RawDepthValue with 27729 elements.
Creating vector time with 27729 elements.
Creating vector RawTempValue with 27729 elements.
Creating vector time with 27729 elements.
Creating vector Temperature with 27729 elements.
Creating vector time with 27729 elements.
Creating vector ErrorValue with 27729 elements.
Creating vector time with 27729 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/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/2005/2005182/2005.182.02/ctdDriver.nc')
Creating vector time with 27654 elements.
Creating vector conductivity with 27654 elements.
Creating vector time with 27654 elements.
Creating vector temperature with 27654 elements.
Creating vector time with 27654 elements.
Creating vector cond_frequency with 27654 elements.
Creating vector time with 27654 elements.
Creating vector temp_frequency with 27654 elements.
Creating vector time with 27654 elements.
Creating vector spare with 27654 elements.
Creating vector time with 27654 elements.
Creating vector humidity with 27654 elements.
Creating vector time with 27654 elements.
Creating vector flow1 with 27654 elements.
Creating vector time with 27654 elements.
Creating vector OBS with 27654 elements.
Creating vector time with 27654 elements.
Creating vector dissolvedO2 with 27654 elements.
Creating vector time with 27654 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/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/2005/2005182/2005.182.02/ctdDriver2.nc')
Creating vector time with 27654 elements.
Creating vector conductivity with 27654 elements.
Creating vector time with 27654 elements.
Creating vector temperature with 27654 elements.
Creating vector time with 27654 elements.
Creating vector cond_frequency with 27654 elements.
Creating vector time with 27654 elements.
Creating vector temp_frequency with 27654 elements.
Creating vector time with 27654 elements.
Creating vector flow2 with 27654 elements.
Creating vector time with 27654 elements.
Creating vector spare with 27654 elements.
Creating vector time with 27654 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/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/2005/2005182/2005.182.02/isuslog.nc')
Creating vector time with 4619 elements.
Creating vector isusNitrate with 4619 elements.
Creating vector time with 4619 elements.
Creating vector isusTemp with 4619 elements.
Creating vector time with 4619 elements.
Creating vector isusQuality with 4619 elements.
Creating vector time with 4619 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/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/2005/2005182/2005.182.02/biolume.nc')
Creating vector time with 6942 elements.
Creating vector rrr with 6942 elements.
Creating vector time with 6942 elements.
Creating vector cal_striing with 6942 elements.
Creating vector time with 6942 elements.
Creating vector pump with 6942 elements.
Creating vector time with 6942 elements.
Creating vector flow with 6942 elements.
Creating vector time with 6942 elements.
Creating vector humidity with 6942 elements.
Creating vector time with 6942 elements.
Creating vector temperature with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_0 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_1 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_2 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_3 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_4 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_5 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_6 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_7 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_8 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_9 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_10 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_11 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_12 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_13 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_14 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_15 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_16 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_17 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_18 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_19 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_20 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_21 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_22 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_23 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_24 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_25 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_26 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_27 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_28 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_29 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_30 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_31 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_32 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_33 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_34 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_35 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_36 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_37 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_38 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_39 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_40 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_41 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_42 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_43 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_44 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_45 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_46 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_47 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_48 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_49 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_50 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_51 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_52 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_53 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_54 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_55 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_56 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_57 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_58 with 6942 elements.
Creating vector time with 6942 elements.
Creating vector raw_59 with 6942 elements.
Creating vector time with 6942 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2005/2005182/2005.182.02/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/2005/2005182/2005.182.02/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/2005/2005182/2005.182.02/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/2005/2005182/2005.182.02/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/2005/2005182/2005.182.02/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_2005.182.02.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_2005.182.00.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.182.01.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.182.02.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 12 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_182_00_182_02_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_182_00_182_02.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_182_00_182_02.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 = 206 Gridding with nix = 618, iZ = 199
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 125084 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 125084 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 119047 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 06/30/2005 18:30  to 07/01/2005 04:29 

swr =

  104.1819
   30.9075
    4.2390
    2.0184
    1.8803
    1.9667
    1.9250
    2.0029
    1.9140
    2.0200
    1.8800

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_182_00_182_02_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2005182_GulperTimes.txt && touch ../results/2005182_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/2005/2005182/2005.182.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005182/2005.182.00/syslog -startEsecs 1120209337.9219 -surveyName Dorado389_2005_182_00_182_02 >> ../results/2005182_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005182_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/2005/2005182/2005.182.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005182/2005.182.01/syslog -startEsecs 1120209337.9219 -surveyName Dorado389_2005_182_00_182_02 >> ../results/2005182_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005182_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/2005/2005182/2005.182.02/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2005/2005182/2005.182.02/syslog -startEsecs 1120209337.9219 -surveyName Dorado389_2005_182_00_182_02 >> ../results/2005182_GulperTimes.txt
Executing: removeGulpDups.py ../results/2005182_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_182_00_182_02_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_182_00_182_02_2column.png
Elapsed time to save image: 12 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_182_00_182_02_biolume.png
Elapsed time to save image: 44 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_182_00_182_02_lopc.png
Elapsed time to save image: 10 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_182_00_182_02_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_182_00_182_02_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_182_00_182_02_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_182_00_182_02_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_182_00_182_02_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_182_00_182_02_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_182_00_182_02_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_182_00_182_02_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_182_00_182_02_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_182_00_182_02_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_182_00_182_02_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_182_00_182_02_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_182_00_182_02_Nitrate.kml (deflated 92%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_182_00_182_02_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_182_00_182_02_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_182_00_182_02_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_182_00_182_02_Optical_Backscatter_470_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_182_00_182_02_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_182_00_182_02_Optical_Backscatter_676_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_182_00_182_02_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_182_00_182_02_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_182_00_182_02_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_182_00_182_02_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_182_00_182_02_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_182_00_182_02_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2005_182_00_182_02_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_182_00_182_02.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_182_00_182_02.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_182_00_182_02_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_182_00_182_02.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
7 NaNs found in bbpRed.  Interpolating anyway.
Encountered 816 NaN values in array of lon that is 17532 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 16716 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 16716 are not equal to number of Lat lon points = 17532
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_182_00_182_02.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005_182_00_182_02.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_182_00_182_02_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_182_00_182_02_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
7 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_182_00_182_02_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_182_00_182_02.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_182_00_182_02_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_182_00_182_02.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_182_00_182_02 processed" mccann@mbari.org < mail_Dorado389_2005_182_00_182_02.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.182.00.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.182.01.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2005.182.02.mat
Processing time: 282 seconds