Execution of AUVprocess_main version 1.86 at 2018-05-23T18:52:12Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2010, ['257.01';'257.02';'257.10';'257.11';'258.00';'258.01';'258.02';'258.03';'258.04'], '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: 2010.257.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/
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/2010/2010257/2010.257.01/navigation.nc')
Creating vector time with 9425 elements.
Creating vector mPos_x with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mPos_y with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mDepth with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mGpsNorth with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mGpsEast with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mGpsValid with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mPhi with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mTheta with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mPsi with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mOmega_x with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mOmega_y with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mOmega_z with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mPsaRange with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mAltitude with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mDvlAltitude with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mWaterSpeed with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mDvlValid with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mDvlNewData with 9425 elements.
Creating vector time with 9425 elements.
Creating vector mDeltaT with 9425 elements.
Creating vector time with 9425 elements.
Creating vector nfix with 9425 elements.
Creating vector time with 9425 elements.
Creating vector efix with 9425 elements.
Creating vector time with 9425 elements.
Creating vector filter_north with 9425 elements.
Creating vector time with 9425 elements.
Creating vector filter_east with 9425 elements.
Creating vector time with 9425 elements.
Creating vector filter_depth with 9425 elements.
Creating vector time with 9425 elements.
Creating vector north_current with 9425 elements.
Creating vector time with 9425 elements.
Creating vector east_current with 9425 elements.
Creating vector time with 9425 elements.
Creating vector speed_bias with 9425 elements.
Creating vector time with 9425 elements.
Creating vector heading_bias with 9425 elements.
Creating vector time with 9425 elements.
Creating vector latitude with 9425 elements.
Creating vector time with 9425 elements.
Creating vector longitude with 9425 elements.
Creating vector time with 9425 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/navigation.nc');
processNav(): median of positive valued depths = 40.3801
processNav(): Finding depths less than 282.6609 and times > 0
processNav(): length(Nav.depth) = 9425
processNav(): length(gindx)     = 9425
 
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/2010/2010257/2010.257.01/gps.nc')
Creating vector time with 486 elements.
Creating vector hours with 486 elements.
Creating vector time with 486 elements.
Creating vector minutes with 486 elements.
Creating vector time with 486 elements.
Creating vector seconds with 486 elements.
Creating vector time with 486 elements.
Creating vector centiSeconds with 486 elements.
Creating vector time with 486 elements.
Creating vector latitude with 486 elements.
Creating vector time with 486 elements.
Creating vector longitude with 486 elements.
Creating vector time with 486 elements.
Creating vector quality with 486 elements.
Creating vector time with 486 elements.
Creating vector numberOfSatellites with 486 elements.
Creating vector time with 486 elements.
Creating vector hdop with 486 elements.
Creating vector time with 486 elements.
Creating vector antennaHeight with 486 elements.
Creating vector time with 486 elements.
Creating vector geoHeight with 486 elements.
Creating vector time with 486 elements.
Creating vector dgpsDataAge with 486 elements.
Creating vector time with 486 elements.
Creating vector dgpsRSID with 486 elements.
Creating vector time with 486 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/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/2010/2010257/2010.257.01/parosci.nc')
Creating vector time with 15324 elements.
Creating vector depth with 15324 elements.
Creating vector time with 15324 elements.
Creating vector temp with 15324 elements.
Creating vector time with 15324 elements.
Creating vector pressure with 15324 elements.
Creating vector time with 15324 elements.
Creating vector temp_period with 15324 elements.
Creating vector time with 15324 elements.
Creating vector pres_period with 15324 elements.
Creating vector time with 15324 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.36518 max(Depth.data) = 100.6269
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.36518 max(Depth.data) = 100.6269
 
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/2010/2010257/2010.257.01/hydroscatlog.nc')
Creating vector time with 7716 elements.
Creating vector Seconds with 7716 elements.
Creating vector time with 7716 elements.
Creating vector HundrethsOfSeconds with 7716 elements.
Creating vector time with 7716 elements.
Creating vector Snorm1 with 7716 elements.
Creating vector time with 7716 elements.
Creating vector Snorm2 with 7716 elements.
Creating vector time with 7716 elements.
Creating vector Snorm3 with 7716 elements.
Creating vector time with 7716 elements.
Creating vector Gain_Status_1 with 7716 elements.
Creating vector time with 7716 elements.
Creating vector Gain_Status_2 with 7716 elements.
Creating vector time with 7716 elements.
Creating vector Gain_Status_3 with 7716 elements.
Creating vector time with 7716 elements.
Creating vector RawDepthValue with 7716 elements.
Creating vector time with 7716 elements.
Creating vector RawTempValue with 7716 elements.
Creating vector time with 7716 elements.
Creating vector Temperature with 7716 elements.
Creating vector time with 7716 elements.
Creating vector ErrorValue with 7716 elements.
Creating vector time with 7716 elements.
Creating vector bb470 with 7716 elements.
Creating vector time with 7716 elements.
Creating vector bb676 with 7716 elements.
Creating vector time with 7716 elements.
Creating vector fl676u with 7716 elements.
Creating vector time with 7716 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/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/2010/2010257/2010.257.01/ctdDriver.nc')
Creating vector time with 7666 elements.
Creating vector conductivity with 7666 elements.
Creating vector time with 7666 elements.
Creating vector temperature with 7666 elements.
Creating vector time with 7666 elements.
Creating vector cond_frequency with 7666 elements.
Creating vector time with 7666 elements.
Creating vector temp_frequency with 7666 elements.
Creating vector time with 7666 elements.
Creating vector spare with 7666 elements.
Creating vector time with 7666 elements.
Creating vector humidity with 7666 elements.
Creating vector time with 7666 elements.
Creating vector flow1 with 7666 elements.
Creating vector time with 7666 elements.
Creating vector rhodamine with 7666 elements.
Creating vector time with 7666 elements.
Creating vector dissolvedO2 with 7666 elements.
Creating vector time with 7666 elements.
Creating vector salinity with 7666 elements.
Creating vector time with 7666 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/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/2010/2010257/2010.257.01/ctdDriver2.nc')
Creating vector time with 7665 elements.
Creating vector conductivity with 7665 elements.
Creating vector time with 7665 elements.
Creating vector temperature with 7665 elements.
Creating vector time with 7665 elements.
Creating vector cond_frequency with 7665 elements.
Creating vector time with 7665 elements.
Creating vector temp_frequency with 7665 elements.
Creating vector time with 7665 elements.
Creating vector flow2 with 7665 elements.
Creating vector time with 7665 elements.
Creating vector spare with 7665 elements.
Creating vector time with 7665 elements.
Creating vector salinity with 7665 elements.
Creating vector time with 7665 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/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/2010/2010257/2010.257.01/isuslog.nc')
Creating vector time with 1452 elements.
Creating vector isusNitrate with 1452 elements.
Creating vector time with 1452 elements.
Creating vector isusTemp with 1452 elements.
Creating vector time with 1452 elements.
Creating vector isusQuality with 1452 elements.
Creating vector time with 1452 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/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/2010/2010257/2010.257.01/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (167 x 994) with 165998 elements.
Creating vector time with 167 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (167 x 994) with 165998 elements.
Creating vector time with 167 elements.
Creating vector bin with 994 elements.
Creating matrix countList (167 x 994) with 165998 elements.
Creating vector time with 167 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 167 elements.
Creating vector time with 167 elements.
Creating vector transCount with 167 elements.
Creating vector time with 167 elements.
Creating vector nonTransCount with 167 elements.
Creating vector time with 167 elements.
Creating vector ai_mean with 167 elements.
Creating vector time with 167 elements.
Creating vector ai_min with 167 elements.
Creating vector time with 167 elements.
Creating vector ai_max with 167 elements.
Creating vector time with 167 elements.
Creating vector ai_std with 167 elements.
Creating vector time with 167 elements.
Creating vector esd_mean with 167 elements.
Creating vector time with 167 elements.
Creating vector esd_min with 167 elements.
Creating vector time with 167 elements.
Creating vector esd_max with 167 elements.
Creating vector time with 167 elements.
Creating vector esd_std with 167 elements.
Creating vector time with 167 elements.
Creating vector countSum with 167 elements.
Creating vector time with 167 elements.
Creating vector snapshot with 167 elements.
Creating vector time with 167 elements.
Creating vector threshold with 167 elements.
Creating vector time with 167 elements.
Creating vector sampleCount with 167 elements.
Creating vector time with 167 elements.
Creating vector flowCount with 167 elements.
Creating vector time with 167 elements.
Creating vector flowTime with 167 elements.
Creating vector time with 167 elements.
Creating vector bufferStatus with 167 elements.
Creating vector time with 167 elements.
Creating vector laserLevel with 167 elements.
Creating vector time with 167 elements.
Creating vector counter with 167 elements.
Creating vector time with 167 elements.
Creating vector counterPeriod with 167 elements.
Creating vector time with 167 elements.
Creating vector laserControl with 167 elements.
Creating vector time with 167 elements.
Creating vector countUnknownFrameCharacter with 167 elements.
Creating vector time with 167 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 167 elements.
Creating vector time with 167 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 167 elements.
Creating vector time with 167 elements.
Creating vector flowSpeed with 167 elements.
Creating vector time with 167 elements.
Creating vector countShortLFrameError with 167 elements.
Creating vector time with 167 elements.
Creating vector countGarbledLFrame with 167 elements.
Creating vector time with 167 elements.
Creating vector cFrameEsecs with 167 elements.
Creating vector time with 167 elements.
Creating vector correctedSampleCountList with 167 elements.
Creating vector time with 167 elements.
Creating vector time with 167 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.01/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.257.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
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Processing AUV mission: 2010.257.02
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/
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/2010/2010257/2010.257.02/navigation.nc')
Creating vector time with 7306 elements.
Creating vector mPos_x with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mPos_y with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mDepth with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mGpsNorth with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mGpsEast with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mGpsValid with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mPhi with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mTheta with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mPsi with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mOmega_x with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mOmega_y with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mOmega_z with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mPsaRange with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mAltitude with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mDvlAltitude with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mWaterSpeed with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mDvlValid with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mDvlNewData with 7306 elements.
Creating vector time with 7306 elements.
Creating vector mDeltaT with 7306 elements.
Creating vector time with 7306 elements.
Creating vector nfix with 7306 elements.
Creating vector time with 7306 elements.
Creating vector efix with 7306 elements.
Creating vector time with 7306 elements.
Creating vector filter_north with 7306 elements.
Creating vector time with 7306 elements.
Creating vector filter_east with 7306 elements.
Creating vector time with 7306 elements.
Creating vector filter_depth with 7306 elements.
Creating vector time with 7306 elements.
Creating vector north_current with 7306 elements.
Creating vector time with 7306 elements.
Creating vector east_current with 7306 elements.
Creating vector time with 7306 elements.
Creating vector speed_bias with 7306 elements.
Creating vector time with 7306 elements.
Creating vector heading_bias with 7306 elements.
Creating vector time with 7306 elements.
Creating vector latitude with 7306 elements.
Creating vector time with 7306 elements.
Creating vector longitude with 7306 elements.
Creating vector time with 7306 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/navigation.nc');
processNav(): median of positive valued depths = 49.201
processNav(): Finding depths less than 344.4068 and times > 0
processNav(): length(Nav.depth) = 7306
processNav(): length(gindx)     = 7306
 
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/2010/2010257/2010.257.02/gps.nc')
Creating vector time with 223 elements.
Creating vector hours with 223 elements.
Creating vector time with 223 elements.
Creating vector minutes with 223 elements.
Creating vector time with 223 elements.
Creating vector seconds with 223 elements.
Creating vector time with 223 elements.
Creating vector centiSeconds with 223 elements.
Creating vector time with 223 elements.
Creating vector latitude with 223 elements.
Creating vector time with 223 elements.
Creating vector longitude with 223 elements.
Creating vector time with 223 elements.
Creating vector quality with 223 elements.
Creating vector time with 223 elements.
Creating vector numberOfSatellites with 223 elements.
Creating vector time with 223 elements.
Creating vector hdop with 223 elements.
Creating vector time with 223 elements.
Creating vector antennaHeight with 223 elements.
Creating vector time with 223 elements.
Creating vector geoHeight with 223 elements.
Creating vector time with 223 elements.
Creating vector dgpsDataAge with 223 elements.
Creating vector time with 223 elements.
Creating vector dgpsRSID with 223 elements.
Creating vector time with 223 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/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/2010/2010257/2010.257.02/parosci.nc')
Creating vector time with 10810 elements.
Creating vector depth with 10810 elements.
Creating vector time with 10810 elements.
Creating vector temp with 10810 elements.
Creating vector time with 10810 elements.
Creating vector pressure with 10810 elements.
Creating vector time with 10810 elements.
Creating vector temp_period with 10810 elements.
Creating vector time with 10810 elements.
Creating vector pres_period with 10810 elements.
Creating vector time with 10810 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.16731 max(Depth.data) = 100.6226
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.16731 max(Depth.data) = 100.6226
 
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/2010/2010257/2010.257.02/hydroscatlog.nc')
Creating vector time with 6018 elements.
Creating vector Seconds with 6018 elements.
Creating vector time with 6018 elements.
Creating vector HundrethsOfSeconds with 6018 elements.
Creating vector time with 6018 elements.
Creating vector Snorm1 with 6018 elements.
Creating vector time with 6018 elements.
Creating vector Snorm2 with 6018 elements.
Creating vector time with 6018 elements.
Creating vector Snorm3 with 6018 elements.
Creating vector time with 6018 elements.
Creating vector Gain_Status_1 with 6018 elements.
Creating vector time with 6018 elements.
Creating vector Gain_Status_2 with 6018 elements.
Creating vector time with 6018 elements.
Creating vector Gain_Status_3 with 6018 elements.
Creating vector time with 6018 elements.
Creating vector RawDepthValue with 6018 elements.
Creating vector time with 6018 elements.
Creating vector RawTempValue with 6018 elements.
Creating vector time with 6018 elements.
Creating vector Temperature with 6018 elements.
Creating vector time with 6018 elements.
Creating vector ErrorValue with 6018 elements.
Creating vector time with 6018 elements.
Creating vector bb470 with 6018 elements.
Creating vector time with 6018 elements.
Creating vector bb676 with 6018 elements.
Creating vector time with 6018 elements.
Creating vector fl676u with 6018 elements.
Creating vector time with 6018 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/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/2010/2010257/2010.257.02/ctdDriver.nc')
Creating vector time with 5934 elements.
Creating vector conductivity with 5934 elements.
Creating vector time with 5934 elements.
Creating vector temperature with 5934 elements.
Creating vector time with 5934 elements.
Creating vector cond_frequency with 5934 elements.
Creating vector time with 5934 elements.
Creating vector temp_frequency with 5934 elements.
Creating vector time with 5934 elements.
Creating vector spare with 5934 elements.
Creating vector time with 5934 elements.
Creating vector humidity with 5934 elements.
Creating vector time with 5934 elements.
Creating vector flow1 with 5934 elements.
Creating vector time with 5934 elements.
Creating vector rhodamine with 5934 elements.
Creating vector time with 5934 elements.
Creating vector dissolvedO2 with 5934 elements.
Creating vector time with 5934 elements.
Creating vector salinity with 5934 elements.
Creating vector time with 5934 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/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/2010/2010257/2010.257.02/ctdDriver2.nc')
Creating vector time with 5932 elements.
Creating vector conductivity with 5932 elements.
Creating vector time with 5932 elements.
Creating vector temperature with 5932 elements.
Creating vector time with 5932 elements.
Creating vector cond_frequency with 5932 elements.
Creating vector time with 5932 elements.
Creating vector temp_frequency with 5932 elements.
Creating vector time with 5932 elements.
Creating vector flow2 with 5932 elements.
Creating vector time with 5932 elements.
Creating vector spare with 5932 elements.
Creating vector time with 5932 elements.
Creating vector salinity with 5932 elements.
Creating vector time with 5932 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/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/2010/2010257/2010.257.02/isuslog.nc')
Creating vector time with 1120 elements.
Creating vector isusNitrate with 1120 elements.
Creating vector time with 1120 elements.
Creating vector isusTemp with 1120 elements.
Creating vector time with 1120 elements.
Creating vector isusQuality with 1120 elements.
Creating vector time with 1120 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/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/2010/2010257/2010.257.02/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (137 x 994) with 136178 elements.
Creating vector time with 137 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (137 x 994) with 136178 elements.
Creating vector time with 137 elements.
Creating vector bin with 994 elements.
Creating matrix countList (137 x 994) with 136178 elements.
Creating vector time with 137 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 137 elements.
Creating vector time with 137 elements.
Creating vector transCount with 137 elements.
Creating vector time with 137 elements.
Creating vector nonTransCount with 137 elements.
Creating vector time with 137 elements.
Creating vector ai_mean with 137 elements.
Creating vector time with 137 elements.
Creating vector ai_min with 137 elements.
Creating vector time with 137 elements.
Creating vector ai_max with 137 elements.
Creating vector time with 137 elements.
Creating vector ai_std with 137 elements.
Creating vector time with 137 elements.
Creating vector esd_mean with 137 elements.
Creating vector time with 137 elements.
Creating vector esd_min with 137 elements.
Creating vector time with 137 elements.
Creating vector esd_max with 137 elements.
Creating vector time with 137 elements.
Creating vector esd_std with 137 elements.
Creating vector time with 137 elements.
Creating vector countSum with 137 elements.
Creating vector time with 137 elements.
Creating vector snapshot with 137 elements.
Creating vector time with 137 elements.
Creating vector threshold with 137 elements.
Creating vector time with 137 elements.
Creating vector sampleCount with 137 elements.
Creating vector time with 137 elements.
Creating vector flowCount with 137 elements.
Creating vector time with 137 elements.
Creating vector flowTime with 137 elements.
Creating vector time with 137 elements.
Creating vector bufferStatus with 137 elements.
Creating vector time with 137 elements.
Creating vector laserLevel with 137 elements.
Creating vector time with 137 elements.
Creating vector counter with 137 elements.
Creating vector time with 137 elements.
Creating vector counterPeriod with 137 elements.
Creating vector time with 137 elements.
Creating vector laserControl with 137 elements.
Creating vector time with 137 elements.
Creating vector countUnknownFrameCharacter with 137 elements.
Creating vector time with 137 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 137 elements.
Creating vector time with 137 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 137 elements.
Creating vector time with 137 elements.
Creating vector flowSpeed with 137 elements.
Creating vector time with 137 elements.
Creating vector countShortLFrameError with 137 elements.
Creating vector time with 137 elements.
Creating vector countGarbledLFrame with 137 elements.
Creating vector time with 137 elements.
Creating vector cFrameEsecs with 137 elements.
Creating vector time with 137 elements.
Creating vector correctedSampleCountList with 137 elements.
Creating vector time with 137 elements.
Creating vector time with 137 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.02/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.257.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2010.257.10
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/
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/2010/2010257/2010.257.10/navigation.nc')
Creating vector time with 2816 elements.
Creating vector mPos_x with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mPos_y with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mDepth with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mGpsNorth with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mGpsEast with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mGpsValid with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mPhi with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mTheta with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mPsi with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mOmega_x with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mOmega_y with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mOmega_z with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mPsaRange with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mAltitude with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mDvlAltitude with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mWaterSpeed with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mDvlValid with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mDvlNewData with 2816 elements.
Creating vector time with 2816 elements.
Creating vector mDeltaT with 2816 elements.
Creating vector time with 2816 elements.
Creating vector nfix with 2816 elements.
Creating vector time with 2816 elements.
Creating vector efix with 2816 elements.
Creating vector time with 2816 elements.
Creating vector filter_north with 2816 elements.
Creating vector time with 2816 elements.
Creating vector filter_east with 2816 elements.
Creating vector time with 2816 elements.
Creating vector filter_depth with 2816 elements.
Creating vector time with 2816 elements.
Creating vector north_current with 2816 elements.
Creating vector time with 2816 elements.
Creating vector east_current with 2816 elements.
Creating vector time with 2816 elements.
Creating vector speed_bias with 2816 elements.
Creating vector time with 2816 elements.
Creating vector heading_bias with 2816 elements.
Creating vector time with 2816 elements.
Creating vector latitude with 2816 elements.
Creating vector time with 2816 elements.
Creating vector longitude with 2816 elements.
Creating vector time with 2816 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/navigation.nc');
processNav(): median of positive valued depths = 19.6687
processNav(): Finding depths less than 137.6806 and times > 0
processNav(): length(Nav.depth) = 2816
processNav(): length(gindx)     = 2816
 
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/2010/2010257/2010.257.10/gps.nc')
Creating vector time with 278 elements.
Creating vector hours with 278 elements.
Creating vector time with 278 elements.
Creating vector minutes with 278 elements.
Creating vector time with 278 elements.
Creating vector seconds with 278 elements.
Creating vector time with 278 elements.
Creating vector centiSeconds with 278 elements.
Creating vector time with 278 elements.
Creating vector latitude with 278 elements.
Creating vector time with 278 elements.
Creating vector longitude with 278 elements.
Creating vector time with 278 elements.
Creating vector quality with 278 elements.
Creating vector time with 278 elements.
Creating vector numberOfSatellites with 278 elements.
Creating vector time with 278 elements.
Creating vector hdop with 278 elements.
Creating vector time with 278 elements.
Creating vector antennaHeight with 278 elements.
Creating vector time with 278 elements.
Creating vector geoHeight with 278 elements.
Creating vector time with 278 elements.
Creating vector dgpsDataAge with 278 elements.
Creating vector time with 278 elements.
Creating vector dgpsRSID with 278 elements.
Creating vector time with 278 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/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/2010/2010257/2010.257.10/parosci.nc')
Creating vector time with 4561 elements.
Creating vector depth with 4561 elements.
Creating vector time with 4561 elements.
Creating vector temp with 4561 elements.
Creating vector time with 4561 elements.
Creating vector pressure with 4561 elements.
Creating vector time with 4561 elements.
Creating vector temp_period with 4561 elements.
Creating vector time with 4561 elements.
Creating vector pres_period with 4561 elements.
Creating vector time with 4561 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.16851 max(Depth.data) = 35.7438
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.16851 max(Depth.data) = 35.7438
 
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/2010/2010257/2010.257.10/hydroscatlog.nc')
Creating vector time with 2427 elements.
Creating vector Seconds with 2427 elements.
Creating vector time with 2427 elements.
Creating vector HundrethsOfSeconds with 2427 elements.
Creating vector time with 2427 elements.
Creating vector Snorm1 with 2427 elements.
Creating vector time with 2427 elements.
Creating vector Snorm2 with 2427 elements.
Creating vector time with 2427 elements.
Creating vector Snorm3 with 2427 elements.
Creating vector time with 2427 elements.
Creating vector Gain_Status_1 with 2427 elements.
Creating vector time with 2427 elements.
Creating vector Gain_Status_2 with 2427 elements.
Creating vector time with 2427 elements.
Creating vector Gain_Status_3 with 2427 elements.
Creating vector time with 2427 elements.
Creating vector RawDepthValue with 2427 elements.
Creating vector time with 2427 elements.
Creating vector RawTempValue with 2427 elements.
Creating vector time with 2427 elements.
Creating vector Temperature with 2427 elements.
Creating vector time with 2427 elements.
Creating vector ErrorValue with 2427 elements.
Creating vector time with 2427 elements.
Creating vector bb470 with 2427 elements.
Creating vector time with 2427 elements.
Creating vector bb676 with 2427 elements.
Creating vector time with 2427 elements.
Creating vector fl676u with 2427 elements.
Creating vector time with 2427 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/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/2010/2010257/2010.257.10/ctdDriver.nc')
Creating vector time with 2346 elements.
Creating vector conductivity with 2346 elements.
Creating vector time with 2346 elements.
Creating vector temperature with 2346 elements.
Creating vector time with 2346 elements.
Creating vector cond_frequency with 2346 elements.
Creating vector time with 2346 elements.
Creating vector temp_frequency with 2346 elements.
Creating vector time with 2346 elements.
Creating vector spare with 2346 elements.
Creating vector time with 2346 elements.
Creating vector humidity with 2346 elements.
Creating vector time with 2346 elements.
Creating vector flow1 with 2346 elements.
Creating vector time with 2346 elements.
Creating vector rhodamine with 2346 elements.
Creating vector time with 2346 elements.
Creating vector dissolvedO2 with 2346 elements.
Creating vector time with 2346 elements.
Creating vector salinity with 2346 elements.
Creating vector time with 2346 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/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/2010/2010257/2010.257.10/ctdDriver2.nc')
Creating vector time with 2342 elements.
Creating vector conductivity with 2342 elements.
Creating vector time with 2342 elements.
Creating vector temperature with 2342 elements.
Creating vector time with 2342 elements.
Creating vector cond_frequency with 2342 elements.
Creating vector time with 2342 elements.
Creating vector temp_frequency with 2342 elements.
Creating vector time with 2342 elements.
Creating vector flow2 with 2342 elements.
Creating vector time with 2342 elements.
Creating vector spare with 2342 elements.
Creating vector time with 2342 elements.
Creating vector salinity with 2342 elements.
Creating vector time with 2342 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/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/2010/2010257/2010.257.10/isuslog.nc')
Creating vector time with 419 elements.
Creating vector isusNitrate with 419 elements.
Creating vector time with 419 elements.
Creating vector isusTemp with 419 elements.
Creating vector time with 419 elements.
Creating vector isusQuality with 419 elements.
Creating vector time with 419 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/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/2010/2010257/2010.257.10/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (56 x 994) with 55664 elements.
Creating vector time with 56 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (56 x 994) with 55664 elements.
Creating vector time with 56 elements.
Creating vector bin with 994 elements.
Creating matrix countList (56 x 994) with 55664 elements.
Creating vector time with 56 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 56 elements.
Creating vector time with 56 elements.
Creating vector transCount with 56 elements.
Creating vector time with 56 elements.
Creating vector nonTransCount with 56 elements.
Creating vector time with 56 elements.
Creating vector ai_mean with 56 elements.
Creating vector time with 56 elements.
Creating vector ai_min with 56 elements.
Creating vector time with 56 elements.
Creating vector ai_max with 56 elements.
Creating vector time with 56 elements.
Creating vector ai_std with 56 elements.
Creating vector time with 56 elements.
Creating vector esd_mean with 56 elements.
Creating vector time with 56 elements.
Creating vector esd_min with 56 elements.
Creating vector time with 56 elements.
Creating vector esd_max with 56 elements.
Creating vector time with 56 elements.
Creating vector esd_std with 56 elements.
Creating vector time with 56 elements.
Creating vector countSum with 56 elements.
Creating vector time with 56 elements.
Creating vector snapshot with 56 elements.
Creating vector time with 56 elements.
Creating vector threshold with 56 elements.
Creating vector time with 56 elements.
Creating vector sampleCount with 56 elements.
Creating vector time with 56 elements.
Creating vector flowCount with 56 elements.
Creating vector time with 56 elements.
Creating vector flowTime with 56 elements.
Creating vector time with 56 elements.
Creating vector bufferStatus with 56 elements.
Creating vector time with 56 elements.
Creating vector laserLevel with 56 elements.
Creating vector time with 56 elements.
Creating vector counter with 56 elements.
Creating vector time with 56 elements.
Creating vector counterPeriod with 56 elements.
Creating vector time with 56 elements.
Creating vector laserControl with 56 elements.
Creating vector time with 56 elements.
Creating vector countUnknownFrameCharacter with 56 elements.
Creating vector time with 56 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 56 elements.
Creating vector time with 56 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 56 elements.
Creating vector time with 56 elements.
Creating vector flowSpeed with 56 elements.
Creating vector time with 56 elements.
Creating vector countShortLFrameError with 56 elements.
Creating vector time with 56 elements.
Creating vector countGarbledLFrame with 56 elements.
Creating vector time with 56 elements.
Creating vector cFrameEsecs with 56 elements.
Creating vector time with 56 elements.
Creating vector correctedSampleCountList with 56 elements.
Creating vector time with 56 elements.
Creating vector time with 56 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.10/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.257.10.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2010.257.11
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/
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/2010/2010257/2010.257.11/navigation.nc')
Creating vector time with 7273 elements.
Creating vector mPos_x with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mPos_y with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mDepth with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mGpsNorth with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mGpsEast with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mGpsValid with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mPhi with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mTheta with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mPsi with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mOmega_x with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mOmega_y with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mOmega_z with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mPsaRange with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mAltitude with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mDvlAltitude with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mWaterSpeed with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mDvlValid with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mDvlNewData with 7273 elements.
Creating vector time with 7273 elements.
Creating vector mDeltaT with 7273 elements.
Creating vector time with 7273 elements.
Creating vector nfix with 7273 elements.
Creating vector time with 7273 elements.
Creating vector efix with 7273 elements.
Creating vector time with 7273 elements.
Creating vector filter_north with 7273 elements.
Creating vector time with 7273 elements.
Creating vector filter_east with 7273 elements.
Creating vector time with 7273 elements.
Creating vector filter_depth with 7273 elements.
Creating vector time with 7273 elements.
Creating vector north_current with 7273 elements.
Creating vector time with 7273 elements.
Creating vector east_current with 7273 elements.
Creating vector time with 7273 elements.
Creating vector speed_bias with 7273 elements.
Creating vector time with 7273 elements.
Creating vector heading_bias with 7273 elements.
Creating vector time with 7273 elements.
Creating vector latitude with 7273 elements.
Creating vector time with 7273 elements.
Creating vector longitude with 7273 elements.
Creating vector time with 7273 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/navigation.nc');
processNav(): median of positive valued depths = 48.9788
processNav(): Finding depths less than 342.8514 and times > 0
processNav(): length(Nav.depth) = 7273
processNav(): length(gindx)     = 7273
 
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/2010/2010257/2010.257.11/gps.nc')
Creating vector time with 192 elements.
Creating vector hours with 192 elements.
Creating vector time with 192 elements.
Creating vector minutes with 192 elements.
Creating vector time with 192 elements.
Creating vector seconds with 192 elements.
Creating vector time with 192 elements.
Creating vector centiSeconds with 192 elements.
Creating vector time with 192 elements.
Creating vector latitude with 192 elements.
Creating vector time with 192 elements.
Creating vector longitude with 192 elements.
Creating vector time with 192 elements.
Creating vector quality with 192 elements.
Creating vector time with 192 elements.
Creating vector numberOfSatellites with 192 elements.
Creating vector time with 192 elements.
Creating vector hdop with 192 elements.
Creating vector time with 192 elements.
Creating vector antennaHeight with 192 elements.
Creating vector time with 192 elements.
Creating vector geoHeight with 192 elements.
Creating vector time with 192 elements.
Creating vector dgpsDataAge with 192 elements.
Creating vector time with 192 elements.
Creating vector dgpsRSID with 192 elements.
Creating vector time with 192 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/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/2010/2010257/2010.257.11/parosci.nc')
Creating vector time with 10551 elements.
Creating vector depth with 10551 elements.
Creating vector time with 10551 elements.
Creating vector temp with 10551 elements.
Creating vector time with 10551 elements.
Creating vector pressure with 10551 elements.
Creating vector time with 10551 elements.
Creating vector temp_period with 10551 elements.
Creating vector time with 10551 elements.
Creating vector pres_period with 10551 elements.
Creating vector time with 10551 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.16814 max(Depth.data) = 100.6467
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.16814 max(Depth.data) = 100.6467
 
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/2010/2010257/2010.257.11/hydroscatlog.nc')
Creating vector time with 5995 elements.
Creating vector Seconds with 5995 elements.
Creating vector time with 5995 elements.
Creating vector HundrethsOfSeconds with 5995 elements.
Creating vector time with 5995 elements.
Creating vector Snorm1 with 5995 elements.
Creating vector time with 5995 elements.
Creating vector Snorm2 with 5995 elements.
Creating vector time with 5995 elements.
Creating vector Snorm3 with 5995 elements.
Creating vector time with 5995 elements.
Creating vector Gain_Status_1 with 5995 elements.
Creating vector time with 5995 elements.
Creating vector Gain_Status_2 with 5995 elements.
Creating vector time with 5995 elements.
Creating vector Gain_Status_3 with 5995 elements.
Creating vector time with 5995 elements.
Creating vector RawDepthValue with 5995 elements.
Creating vector time with 5995 elements.
Creating vector RawTempValue with 5995 elements.
Creating vector time with 5995 elements.
Creating vector Temperature with 5995 elements.
Creating vector time with 5995 elements.
Creating vector ErrorValue with 5995 elements.
Creating vector time with 5995 elements.
Creating vector bb470 with 5995 elements.
Creating vector time with 5995 elements.
Creating vector bb676 with 5995 elements.
Creating vector time with 5995 elements.
Creating vector fl676u with 5995 elements.
Creating vector time with 5995 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/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/2010/2010257/2010.257.11/ctdDriver.nc')
Creating vector time with 5912 elements.
Creating vector conductivity with 5912 elements.
Creating vector time with 5912 elements.
Creating vector temperature with 5912 elements.
Creating vector time with 5912 elements.
Creating vector cond_frequency with 5912 elements.
Creating vector time with 5912 elements.
Creating vector temp_frequency with 5912 elements.
Creating vector time with 5912 elements.
Creating vector spare with 5912 elements.
Creating vector time with 5912 elements.
Creating vector humidity with 5912 elements.
Creating vector time with 5912 elements.
Creating vector flow1 with 5912 elements.
Creating vector time with 5912 elements.
Creating vector rhodamine with 5912 elements.
Creating vector time with 5912 elements.
Creating vector dissolvedO2 with 5912 elements.
Creating vector time with 5912 elements.
Creating vector salinity with 5912 elements.
Creating vector time with 5912 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/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/2010/2010257/2010.257.11/ctdDriver2.nc')
Creating vector time with 5912 elements.
Creating vector conductivity with 5912 elements.
Creating vector time with 5912 elements.
Creating vector temperature with 5912 elements.
Creating vector time with 5912 elements.
Creating vector cond_frequency with 5912 elements.
Creating vector time with 5912 elements.
Creating vector temp_frequency with 5912 elements.
Creating vector time with 5912 elements.
Creating vector flow2 with 5912 elements.
Creating vector time with 5912 elements.
Creating vector spare with 5912 elements.
Creating vector time with 5912 elements.
Creating vector salinity with 5912 elements.
Creating vector time with 5912 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/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/2010/2010257/2010.257.11/isuslog.nc')
Creating vector time with 1116 elements.
Creating vector isusNitrate with 1116 elements.
Creating vector time with 1116 elements.
Creating vector isusTemp with 1116 elements.
Creating vector time with 1116 elements.
Creating vector isusQuality with 1116 elements.
Creating vector time with 1116 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/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/2010/2010257/2010.257.11/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (134 x 994) with 133196 elements.
Creating vector time with 134 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (134 x 994) with 133196 elements.
Creating vector time with 134 elements.
Creating vector bin with 994 elements.
Creating matrix countList (134 x 994) with 133196 elements.
Creating vector time with 134 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 134 elements.
Creating vector time with 134 elements.
Creating vector transCount with 134 elements.
Creating vector time with 134 elements.
Creating vector nonTransCount with 134 elements.
Creating vector time with 134 elements.
Creating vector ai_mean with 134 elements.
Creating vector time with 134 elements.
Creating vector ai_min with 134 elements.
Creating vector time with 134 elements.
Creating vector ai_max with 134 elements.
Creating vector time with 134 elements.
Creating vector ai_std with 134 elements.
Creating vector time with 134 elements.
Creating vector esd_mean with 134 elements.
Creating vector time with 134 elements.
Creating vector esd_min with 134 elements.
Creating vector time with 134 elements.
Creating vector esd_max with 134 elements.
Creating vector time with 134 elements.
Creating vector esd_std with 134 elements.
Creating vector time with 134 elements.
Creating vector countSum with 134 elements.
Creating vector time with 134 elements.
Creating vector snapshot with 134 elements.
Creating vector time with 134 elements.
Creating vector threshold with 134 elements.
Creating vector time with 134 elements.
Creating vector sampleCount with 134 elements.
Creating vector time with 134 elements.
Creating vector flowCount with 134 elements.
Creating vector time with 134 elements.
Creating vector flowTime with 134 elements.
Creating vector time with 134 elements.
Creating vector bufferStatus with 134 elements.
Creating vector time with 134 elements.
Creating vector laserLevel with 134 elements.
Creating vector time with 134 elements.
Creating vector counter with 134 elements.
Creating vector time with 134 elements.
Creating vector counterPeriod with 134 elements.
Creating vector time with 134 elements.
Creating vector laserControl with 134 elements.
Creating vector time with 134 elements.
Creating vector countUnknownFrameCharacter with 134 elements.
Creating vector time with 134 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 134 elements.
Creating vector time with 134 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 134 elements.
Creating vector time with 134 elements.
Creating vector flowSpeed with 134 elements.
Creating vector time with 134 elements.
Creating vector countShortLFrameError with 134 elements.
Creating vector time with 134 elements.
Creating vector countGarbledLFrame with 134 elements.
Creating vector time with 134 elements.
Creating vector cFrameEsecs with 134 elements.
Creating vector time with 134 elements.
Creating vector correctedSampleCountList with 134 elements.
Creating vector time with 134 elements.
Creating vector time with 134 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010257/2010.257.11/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.257.11.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2010.258.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/
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/2010/2010258/2010.258.00/navigation.nc')
Creating vector time with 55815 elements.
Creating vector mPos_x with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mPos_y with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mDepth with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mGpsNorth with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mGpsEast with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mGpsValid with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mPhi with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mTheta with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mPsi with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mOmega_x with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mOmega_y with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mOmega_z with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mPsaRange with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mAltitude with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mDvlAltitude with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mWaterSpeed with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mDvlValid with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mDvlNewData with 55815 elements.
Creating vector time with 55815 elements.
Creating vector mDeltaT with 55815 elements.
Creating vector time with 55815 elements.
Creating vector nfix with 55815 elements.
Creating vector time with 55815 elements.
Creating vector efix with 55815 elements.
Creating vector time with 55815 elements.
Creating vector filter_north with 55815 elements.
Creating vector time with 55815 elements.
Creating vector filter_east with 55815 elements.
Creating vector time with 55815 elements.
Creating vector filter_depth with 55815 elements.
Creating vector time with 55815 elements.
Creating vector north_current with 55815 elements.
Creating vector time with 55815 elements.
Creating vector east_current with 55815 elements.
Creating vector time with 55815 elements.
Creating vector speed_bias with 55815 elements.
Creating vector time with 55815 elements.
Creating vector heading_bias with 55815 elements.
Creating vector time with 55815 elements.
Creating vector latitude with 55815 elements.
Creating vector time with 55815 elements.
Creating vector longitude with 55815 elements.
Creating vector time with 55815 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/navigation.nc');
processNav(): median of positive valued depths = 48.8514
processNav(): Finding depths less than 341.9601 and times > 0
processNav(): length(Nav.depth) = 55815
processNav(): length(gindx)     = 55815
 
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/2010/2010258/2010.258.00/gps.nc')
Creating vector time with 1362 elements.
Creating vector hours with 1362 elements.
Creating vector time with 1362 elements.
Creating vector minutes with 1362 elements.
Creating vector time with 1362 elements.
Creating vector seconds with 1362 elements.
Creating vector time with 1362 elements.
Creating vector centiSeconds with 1362 elements.
Creating vector time with 1362 elements.
Creating vector latitude with 1362 elements.
Creating vector time with 1362 elements.
Creating vector longitude with 1362 elements.
Creating vector time with 1362 elements.
Creating vector quality with 1362 elements.
Creating vector time with 1362 elements.
Creating vector numberOfSatellites with 1362 elements.
Creating vector time with 1362 elements.
Creating vector hdop with 1362 elements.
Creating vector time with 1362 elements.
Creating vector antennaHeight with 1362 elements.
Creating vector time with 1362 elements.
Creating vector geoHeight with 1362 elements.
Creating vector time with 1362 elements.
Creating vector dgpsDataAge with 1362 elements.
Creating vector time with 1362 elements.
Creating vector dgpsRSID with 1362 elements.
Creating vector time with 1362 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/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/2010/2010258/2010.258.00/parosci.nc')
Creating vector time with 91213 elements.
Creating vector depth with 91213 elements.
Creating vector time with 91213 elements.
Creating vector temp with 91213 elements.
Creating vector time with 91213 elements.
Creating vector pressure with 91213 elements.
Creating vector time with 91213 elements.
Creating vector temp_period with 91213 elements.
Creating vector time with 91213 elements.
Creating vector pres_period with 91213 elements.
Creating vector time with 91213 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.27892 max(Depth.data) = 232.4378
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.27892 max(Depth.data) = 232.4378
 
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/2010/2010258/2010.258.00/hydroscatlog.nc')
Creating vector time with 44808 elements.
Creating vector Seconds with 44808 elements.
Creating vector time with 44808 elements.
Creating vector HundrethsOfSeconds with 44808 elements.
Creating vector time with 44808 elements.
Creating vector Snorm1 with 44808 elements.
Creating vector time with 44808 elements.
Creating vector Snorm2 with 44808 elements.
Creating vector time with 44808 elements.
Creating vector Snorm3 with 44808 elements.
Creating vector time with 44808 elements.
Creating vector Gain_Status_1 with 44808 elements.
Creating vector time with 44808 elements.
Creating vector Gain_Status_2 with 44808 elements.
Creating vector time with 44808 elements.
Creating vector Gain_Status_3 with 44808 elements.
Creating vector time with 44808 elements.
Creating vector RawDepthValue with 44808 elements.
Creating vector time with 44808 elements.
Creating vector RawTempValue with 44808 elements.
Creating vector time with 44808 elements.
Creating vector Temperature with 44808 elements.
Creating vector time with 44808 elements.
Creating vector ErrorValue with 44808 elements.
Creating vector time with 44808 elements.
Creating vector bb470 with 44808 elements.
Creating vector time with 44808 elements.
Creating vector bb676 with 44808 elements.
Creating vector time with 44808 elements.
Creating vector fl676u with 44808 elements.
Creating vector time with 44808 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/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/2010/2010258/2010.258.00/ctdDriver.nc')
Creating vector time with 44679 elements.
Creating vector conductivity with 44679 elements.
Creating vector time with 44679 elements.
Creating vector temperature with 44679 elements.
Creating vector time with 44679 elements.
Creating vector cond_frequency with 44679 elements.
Creating vector time with 44679 elements.
Creating vector temp_frequency with 44679 elements.
Creating vector time with 44679 elements.
Creating vector spare with 44679 elements.
Creating vector time with 44679 elements.
Creating vector humidity with 44679 elements.
Creating vector time with 44679 elements.
Creating vector flow1 with 44679 elements.
Creating vector time with 44679 elements.
Creating vector rhodamine with 44679 elements.
Creating vector time with 44679 elements.
Creating vector dissolvedO2 with 44679 elements.
Creating vector time with 44679 elements.
Creating vector salinity with 44679 elements.
Creating vector time with 44679 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/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/2010/2010258/2010.258.00/ctdDriver2.nc')
Creating vector time with 44745 elements.
Creating vector conductivity with 44745 elements.
Creating vector time with 44745 elements.
Creating vector temperature with 44745 elements.
Creating vector time with 44745 elements.
Creating vector cond_frequency with 44745 elements.
Creating vector time with 44745 elements.
Creating vector temp_frequency with 44745 elements.
Creating vector time with 44745 elements.
Creating vector flow2 with 44745 elements.
Creating vector time with 44745 elements.
Creating vector spare with 44745 elements.
Creating vector time with 44745 elements.
Creating vector salinity with 44745 elements.
Creating vector time with 44745 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/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/2010/2010258/2010.258.00/isuslog.nc')
Creating vector time with 8705 elements.
Creating vector isusNitrate with 8705 elements.
Creating vector time with 8705 elements.
Creating vector isusTemp with 8705 elements.
Creating vector time with 8705 elements.
Creating vector isusQuality with 8705 elements.
Creating vector time with 8705 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/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/2010/2010258/2010.258.00/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (1028 x 994) with 1021832 elements.
Creating vector time with 1028 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (1028 x 994) with 1021832 elements.
Creating vector time with 1028 elements.
Creating vector bin with 994 elements.
Creating matrix countList (1028 x 994) with 1021832 elements.
Creating vector time with 1028 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 1028 elements.
Creating vector time with 1028 elements.
Creating vector transCount with 1028 elements.
Creating vector time with 1028 elements.
Creating vector nonTransCount with 1028 elements.
Creating vector time with 1028 elements.
Creating vector ai_mean with 1028 elements.
Creating vector time with 1028 elements.
Creating vector ai_min with 1028 elements.
Creating vector time with 1028 elements.
Creating vector ai_max with 1028 elements.
Creating vector time with 1028 elements.
Creating vector ai_std with 1028 elements.
Creating vector time with 1028 elements.
Creating vector esd_mean with 1028 elements.
Creating vector time with 1028 elements.
Creating vector esd_min with 1028 elements.
Creating vector time with 1028 elements.
Creating vector esd_max with 1028 elements.
Creating vector time with 1028 elements.
Creating vector esd_std with 1028 elements.
Creating vector time with 1028 elements.
Creating vector countSum with 1028 elements.
Creating vector time with 1028 elements.
Creating vector snapshot with 1028 elements.
Creating vector time with 1028 elements.
Creating vector threshold with 1028 elements.
Creating vector time with 1028 elements.
Creating vector sampleCount with 1028 elements.
Creating vector time with 1028 elements.
Creating vector flowCount with 1028 elements.
Creating vector time with 1028 elements.
Creating vector flowTime with 1028 elements.
Creating vector time with 1028 elements.
Creating vector bufferStatus with 1028 elements.
Creating vector time with 1028 elements.
Creating vector laserLevel with 1028 elements.
Creating vector time with 1028 elements.
Creating vector counter with 1028 elements.
Creating vector time with 1028 elements.
Creating vector counterPeriod with 1028 elements.
Creating vector time with 1028 elements.
Creating vector laserControl with 1028 elements.
Creating vector time with 1028 elements.
Creating vector countUnknownFrameCharacter with 1028 elements.
Creating vector time with 1028 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 1028 elements.
Creating vector time with 1028 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 1028 elements.
Creating vector time with 1028 elements.
Creating vector flowSpeed with 1028 elements.
Creating vector time with 1028 elements.
Creating vector countShortLFrameError with 1028 elements.
Creating vector time with 1028 elements.
Creating vector countGarbledLFrame with 1028 elements.
Creating vector time with 1028 elements.
Creating vector cFrameEsecs with 1028 elements.
Creating vector time with 1028 elements.
Creating vector correctedSampleCountList with 1028 elements.
Creating vector time with 1028 elements.
Creating vector time with 1028 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.00/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2010.258.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/
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/2010/2010258/2010.258.01/navigation.nc')
Creating vector time with 33984 elements.
Creating vector mPos_x with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mPos_y with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mDepth with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mGpsNorth with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mGpsEast with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mGpsValid with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mPhi with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mTheta with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mPsi with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mOmega_x with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mOmega_y with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mOmega_z with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mPsaRange with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mAltitude with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mDvlAltitude with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mWaterSpeed with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mDvlValid with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mDvlNewData with 33984 elements.
Creating vector time with 33984 elements.
Creating vector mDeltaT with 33984 elements.
Creating vector time with 33984 elements.
Creating vector nfix with 33984 elements.
Creating vector time with 33984 elements.
Creating vector efix with 33984 elements.
Creating vector time with 33984 elements.
Creating vector filter_north with 33984 elements.
Creating vector time with 33984 elements.
Creating vector filter_east with 33984 elements.
Creating vector time with 33984 elements.
Creating vector filter_depth with 33984 elements.
Creating vector time with 33984 elements.
Creating vector north_current with 33984 elements.
Creating vector time with 33984 elements.
Creating vector east_current with 33984 elements.
Creating vector time with 33984 elements.
Creating vector speed_bias with 33984 elements.
Creating vector time with 33984 elements.
Creating vector heading_bias with 33984 elements.
Creating vector time with 33984 elements.
Creating vector latitude with 33984 elements.
Creating vector time with 33984 elements.
Creating vector longitude with 33984 elements.
Creating vector time with 33984 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/navigation.nc');
processNav(): median of positive valued depths = 49.9757
processNav(): Finding depths less than 349.8302 and times > 0
processNav(): length(Nav.depth) = 33984
processNav(): length(gindx)     = 33984
 
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/2010/2010258/2010.258.01/gps.nc')
Creating vector time with 1217 elements.
Creating vector hours with 1217 elements.
Creating vector time with 1217 elements.
Creating vector minutes with 1217 elements.
Creating vector time with 1217 elements.
Creating vector seconds with 1217 elements.
Creating vector time with 1217 elements.
Creating vector centiSeconds with 1217 elements.
Creating vector time with 1217 elements.
Creating vector latitude with 1217 elements.
Creating vector time with 1217 elements.
Creating vector longitude with 1217 elements.
Creating vector time with 1217 elements.
Creating vector quality with 1217 elements.
Creating vector time with 1217 elements.
Creating vector numberOfSatellites with 1217 elements.
Creating vector time with 1217 elements.
Creating vector hdop with 1217 elements.
Creating vector time with 1217 elements.
Creating vector antennaHeight with 1217 elements.
Creating vector time with 1217 elements.
Creating vector geoHeight with 1217 elements.
Creating vector time with 1217 elements.
Creating vector dgpsDataAge with 1217 elements.
Creating vector time with 1217 elements.
Creating vector dgpsRSID with 1217 elements.
Creating vector time with 1217 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/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/2010/2010258/2010.258.01/parosci.nc')
Creating vector time with 55634 elements.
Creating vector depth with 55634 elements.
Creating vector time with 55634 elements.
Creating vector temp with 55634 elements.
Creating vector time with 55634 elements.
Creating vector pressure with 55634 elements.
Creating vector time with 55634 elements.
Creating vector temp_period with 55634 elements.
Creating vector time with 55634 elements.
Creating vector pres_period with 55634 elements.
Creating vector time with 55634 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.39235 max(Depth.data) = 118.2715
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.39235 max(Depth.data) = 118.2715
 
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/2010/2010258/2010.258.01/hydroscatlog.nc')
Creating vector time with 27348 elements.
Creating vector Seconds with 27348 elements.
Creating vector time with 27348 elements.
Creating vector HundrethsOfSeconds with 27348 elements.
Creating vector time with 27348 elements.
Creating vector Snorm1 with 27348 elements.
Creating vector time with 27348 elements.
Creating vector Snorm2 with 27348 elements.
Creating vector time with 27348 elements.
Creating vector Snorm3 with 27348 elements.
Creating vector time with 27348 elements.
Creating vector Gain_Status_1 with 27348 elements.
Creating vector time with 27348 elements.
Creating vector Gain_Status_2 with 27348 elements.
Creating vector time with 27348 elements.
Creating vector Gain_Status_3 with 27348 elements.
Creating vector time with 27348 elements.
Creating vector RawDepthValue with 27348 elements.
Creating vector time with 27348 elements.
Creating vector RawTempValue with 27348 elements.
Creating vector time with 27348 elements.
Creating vector Temperature with 27348 elements.
Creating vector time with 27348 elements.
Creating vector ErrorValue with 27348 elements.
Creating vector time with 27348 elements.
Creating vector bb470 with 27348 elements.
Creating vector time with 27348 elements.
Creating vector bb676 with 27348 elements.
Creating vector time with 27348 elements.
Creating vector fl676u with 27348 elements.
Creating vector time with 27348 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/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/2010/2010258/2010.258.01/ctdDriver.nc')
Creating vector time with 27308 elements.
Creating vector conductivity with 27308 elements.
Creating vector time with 27308 elements.
Creating vector temperature with 27308 elements.
Creating vector time with 27308 elements.
Creating vector cond_frequency with 27308 elements.
Creating vector time with 27308 elements.
Creating vector temp_frequency with 27308 elements.
Creating vector time with 27308 elements.
Creating vector spare with 27308 elements.
Creating vector time with 27308 elements.
Creating vector humidity with 27308 elements.
Creating vector time with 27308 elements.
Creating vector flow1 with 27308 elements.
Creating vector time with 27308 elements.
Creating vector rhodamine with 27308 elements.
Creating vector time with 27308 elements.
Creating vector dissolvedO2 with 27308 elements.
Creating vector time with 27308 elements.
Creating vector salinity with 27308 elements.
Creating vector time with 27308 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/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/2010/2010258/2010.258.01/ctdDriver2.nc')
Creating vector time with 27308 elements.
Creating vector conductivity with 27308 elements.
Creating vector time with 27308 elements.
Creating vector temperature with 27308 elements.
Creating vector time with 27308 elements.
Creating vector cond_frequency with 27308 elements.
Creating vector time with 27308 elements.
Creating vector temp_frequency with 27308 elements.
Creating vector time with 27308 elements.
Creating vector flow2 with 27308 elements.
Creating vector time with 27308 elements.
Creating vector spare with 27308 elements.
Creating vector time with 27308 elements.
Creating vector salinity with 27308 elements.
Creating vector time with 27308 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/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/2010/2010258/2010.258.01/isuslog.nc')
Creating vector time with 5293 elements.
Creating vector isusNitrate with 5293 elements.
Creating vector time with 5293 elements.
Creating vector isusTemp with 5293 elements.
Creating vector time with 5293 elements.
Creating vector isusQuality with 5293 elements.
Creating vector time with 5293 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/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/2010/2010258/2010.258.01/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (648 x 994) with 644112 elements.
Creating vector time with 648 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (648 x 994) with 644112 elements.
Creating vector time with 648 elements.
Creating vector bin with 994 elements.
Creating matrix countList (648 x 994) with 644112 elements.
Creating vector time with 648 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 648 elements.
Creating vector time with 648 elements.
Creating vector transCount with 648 elements.
Creating vector time with 648 elements.
Creating vector nonTransCount with 648 elements.
Creating vector time with 648 elements.
Creating vector ai_mean with 648 elements.
Creating vector time with 648 elements.
Creating vector ai_min with 648 elements.
Creating vector time with 648 elements.
Creating vector ai_max with 648 elements.
Creating vector time with 648 elements.
Creating vector ai_std with 648 elements.
Creating vector time with 648 elements.
Creating vector esd_mean with 648 elements.
Creating vector time with 648 elements.
Creating vector esd_min with 648 elements.
Creating vector time with 648 elements.
Creating vector esd_max with 648 elements.
Creating vector time with 648 elements.
Creating vector esd_std with 648 elements.
Creating vector time with 648 elements.
Creating vector countSum with 648 elements.
Creating vector time with 648 elements.
Creating vector snapshot with 648 elements.
Creating vector time with 648 elements.
Creating vector threshold with 648 elements.
Creating vector time with 648 elements.
Creating vector sampleCount with 648 elements.
Creating vector time with 648 elements.
Creating vector flowCount with 648 elements.
Creating vector time with 648 elements.
Creating vector flowTime with 648 elements.
Creating vector time with 648 elements.
Creating vector bufferStatus with 648 elements.
Creating vector time with 648 elements.
Creating vector laserLevel with 648 elements.
Creating vector time with 648 elements.
Creating vector counter with 648 elements.
Creating vector time with 648 elements.
Creating vector counterPeriod with 648 elements.
Creating vector time with 648 elements.
Creating vector laserControl with 648 elements.
Creating vector time with 648 elements.
Creating vector countUnknownFrameCharacter with 648 elements.
Creating vector time with 648 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 648 elements.
Creating vector time with 648 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 648 elements.
Creating vector time with 648 elements.
Creating vector flowSpeed with 648 elements.
Creating vector time with 648 elements.
Creating vector countShortLFrameError with 648 elements.
Creating vector time with 648 elements.
Creating vector countGarbledLFrame with 648 elements.
Creating vector time with 648 elements.
Creating vector cFrameEsecs with 648 elements.
Creating vector time with 648 elements.
Creating vector correctedSampleCountList with 648 elements.
Creating vector time with 648 elements.
Creating vector time with 648 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.01/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2010.258.02
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/
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/2010/2010258/2010.258.02/navigation.nc')
Creating vector time with 21888 elements.
Creating vector mPos_x with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mPos_y with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mDepth with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mGpsNorth with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mGpsEast with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mGpsValid with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mPhi with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mTheta with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mPsi with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mOmega_x with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mOmega_y with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mOmega_z with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mPsaRange with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mAltitude with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mDvlAltitude with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mWaterSpeed with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mDvlValid with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mDvlNewData with 21888 elements.
Creating vector time with 21888 elements.
Creating vector mDeltaT with 21888 elements.
Creating vector time with 21888 elements.
Creating vector nfix with 21888 elements.
Creating vector time with 21888 elements.
Creating vector efix with 21888 elements.
Creating vector time with 21888 elements.
Creating vector filter_north with 21888 elements.
Creating vector time with 21888 elements.
Creating vector filter_east with 21888 elements.
Creating vector time with 21888 elements.
Creating vector filter_depth with 21888 elements.
Creating vector time with 21888 elements.
Creating vector north_current with 21888 elements.
Creating vector time with 21888 elements.
Creating vector east_current with 21888 elements.
Creating vector time with 21888 elements.
Creating vector speed_bias with 21888 elements.
Creating vector time with 21888 elements.
Creating vector heading_bias with 21888 elements.
Creating vector time with 21888 elements.
Creating vector latitude with 21888 elements.
Creating vector time with 21888 elements.
Creating vector longitude with 21888 elements.
Creating vector time with 21888 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/navigation.nc');
processNav(): median of positive valued depths = 45.1937
processNav(): Finding depths less than 316.3556 and times > 0
processNav(): length(Nav.depth) = 21888
processNav(): length(gindx)     = 21888
 
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/2010/2010258/2010.258.02/gps.nc')
Creating vector time with 708 elements.
Creating vector hours with 708 elements.
Creating vector time with 708 elements.
Creating vector minutes with 708 elements.
Creating vector time with 708 elements.
Creating vector seconds with 708 elements.
Creating vector time with 708 elements.
Creating vector centiSeconds with 708 elements.
Creating vector time with 708 elements.
Creating vector latitude with 708 elements.
Creating vector time with 708 elements.
Creating vector longitude with 708 elements.
Creating vector time with 708 elements.
Creating vector quality with 708 elements.
Creating vector time with 708 elements.
Creating vector numberOfSatellites with 708 elements.
Creating vector time with 708 elements.
Creating vector hdop with 708 elements.
Creating vector time with 708 elements.
Creating vector antennaHeight with 708 elements.
Creating vector time with 708 elements.
Creating vector geoHeight with 708 elements.
Creating vector time with 708 elements.
Creating vector dgpsDataAge with 708 elements.
Creating vector time with 708 elements.
Creating vector dgpsRSID with 708 elements.
Creating vector time with 708 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/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/2010/2010258/2010.258.02/parosci.nc')
Creating vector time with 35890 elements.
Creating vector depth with 35890 elements.
Creating vector time with 35890 elements.
Creating vector temp with 35890 elements.
Creating vector time with 35890 elements.
Creating vector pressure with 35890 elements.
Creating vector time with 35890 elements.
Creating vector temp_period with 35890 elements.
Creating vector time with 35890 elements.
Creating vector pres_period with 35890 elements.
Creating vector time with 35890 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.24434 max(Depth.data) = 210.1911
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.24434 max(Depth.data) = 210.1911
 
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/2010/2010258/2010.258.02/hydroscatlog.nc')
Creating vector time with 17663 elements.
Creating vector Seconds with 17663 elements.
Creating vector time with 17663 elements.
Creating vector HundrethsOfSeconds with 17663 elements.
Creating vector time with 17663 elements.
Creating vector Snorm1 with 17663 elements.
Creating vector time with 17663 elements.
Creating vector Snorm2 with 17663 elements.
Creating vector time with 17663 elements.
Creating vector Snorm3 with 17663 elements.
Creating vector time with 17663 elements.
Creating vector Gain_Status_1 with 17663 elements.
Creating vector time with 17663 elements.
Creating vector Gain_Status_2 with 17663 elements.
Creating vector time with 17663 elements.
Creating vector Gain_Status_3 with 17663 elements.
Creating vector time with 17663 elements.
Creating vector RawDepthValue with 17663 elements.
Creating vector time with 17663 elements.
Creating vector RawTempValue with 17663 elements.
Creating vector time with 17663 elements.
Creating vector Temperature with 17663 elements.
Creating vector time with 17663 elements.
Creating vector ErrorValue with 17663 elements.
Creating vector time with 17663 elements.
Creating vector bb470 with 17663 elements.
Creating vector time with 17663 elements.
Creating vector bb676 with 17663 elements.
Creating vector time with 17663 elements.
Creating vector fl676u with 17663 elements.
Creating vector time with 17663 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/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/2010/2010258/2010.258.02/ctdDriver.nc')
Creating vector time with 17600 elements.
Creating vector conductivity with 17600 elements.
Creating vector time with 17600 elements.
Creating vector temperature with 17600 elements.
Creating vector time with 17600 elements.
Creating vector cond_frequency with 17600 elements.
Creating vector time with 17600 elements.
Creating vector temp_frequency with 17600 elements.
Creating vector time with 17600 elements.
Creating vector spare with 17600 elements.
Creating vector time with 17600 elements.
Creating vector humidity with 17600 elements.
Creating vector time with 17600 elements.
Creating vector flow1 with 17600 elements.
Creating vector time with 17600 elements.
Creating vector rhodamine with 17600 elements.
Creating vector time with 17600 elements.
Creating vector dissolvedO2 with 17600 elements.
Creating vector time with 17600 elements.
Creating vector salinity with 17600 elements.
Creating vector time with 17600 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/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/2010/2010258/2010.258.02/ctdDriver2.nc')
Creating vector time with 17595 elements.
Creating vector conductivity with 17595 elements.
Creating vector time with 17595 elements.
Creating vector temperature with 17595 elements.
Creating vector time with 17595 elements.
Creating vector cond_frequency with 17595 elements.
Creating vector time with 17595 elements.
Creating vector temp_frequency with 17595 elements.
Creating vector time with 17595 elements.
Creating vector flow2 with 17595 elements.
Creating vector time with 17595 elements.
Creating vector spare with 17595 elements.
Creating vector time with 17595 elements.
Creating vector salinity with 17595 elements.
Creating vector time with 17595 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/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/2010/2010258/2010.258.02/isuslog.nc')
Creating vector time with 3398 elements.
Creating vector isusNitrate with 3398 elements.
Creating vector time with 3398 elements.
Creating vector isusTemp with 3398 elements.
Creating vector time with 3398 elements.
Creating vector isusQuality with 3398 elements.
Creating vector time with 3398 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/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/2010/2010258/2010.258.02/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (413 x 994) with 410522 elements.
Creating vector time with 413 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (413 x 994) with 410522 elements.
Creating vector time with 413 elements.
Creating vector bin with 994 elements.
Creating matrix countList (413 x 994) with 410522 elements.
Creating vector time with 413 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 413 elements.
Creating vector time with 413 elements.
Creating vector transCount with 413 elements.
Creating vector time with 413 elements.
Creating vector nonTransCount with 413 elements.
Creating vector time with 413 elements.
Creating vector ai_mean with 413 elements.
Creating vector time with 413 elements.
Creating vector ai_min with 413 elements.
Creating vector time with 413 elements.
Creating vector ai_max with 413 elements.
Creating vector time with 413 elements.
Creating vector ai_std with 413 elements.
Creating vector time with 413 elements.
Creating vector esd_mean with 413 elements.
Creating vector time with 413 elements.
Creating vector esd_min with 413 elements.
Creating vector time with 413 elements.
Creating vector esd_max with 413 elements.
Creating vector time with 413 elements.
Creating vector esd_std with 413 elements.
Creating vector time with 413 elements.
Creating vector countSum with 413 elements.
Creating vector time with 413 elements.
Creating vector snapshot with 413 elements.
Creating vector time with 413 elements.
Creating vector threshold with 413 elements.
Creating vector time with 413 elements.
Creating vector sampleCount with 413 elements.
Creating vector time with 413 elements.
Creating vector flowCount with 413 elements.
Creating vector time with 413 elements.
Creating vector flowTime with 413 elements.
Creating vector time with 413 elements.
Creating vector bufferStatus with 413 elements.
Creating vector time with 413 elements.
Creating vector laserLevel with 413 elements.
Creating vector time with 413 elements.
Creating vector counter with 413 elements.
Creating vector time with 413 elements.
Creating vector counterPeriod with 413 elements.
Creating vector time with 413 elements.
Creating vector laserControl with 413 elements.
Creating vector time with 413 elements.
Creating vector countUnknownFrameCharacter with 413 elements.
Creating vector time with 413 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 413 elements.
Creating vector time with 413 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 413 elements.
Creating vector time with 413 elements.
Creating vector flowSpeed with 413 elements.
Creating vector time with 413 elements.
Creating vector countShortLFrameError with 413 elements.
Creating vector time with 413 elements.
Creating vector countGarbledLFrame with 413 elements.
Creating vector time with 413 elements.
Creating vector cFrameEsecs with 413 elements.
Creating vector time with 413 elements.
Creating vector correctedSampleCountList with 413 elements.
Creating vector time with 413 elements.
Creating vector time with 413 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.02/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2010.258.03
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/
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/2010/2010258/2010.258.03/navigation.nc')
Creating vector time with 1702 elements.
Creating vector mPos_x with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mPos_y with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mDepth with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mGpsNorth with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mGpsEast with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mGpsValid with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mPhi with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mTheta with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mPsi with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mOmega_x with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mOmega_y with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mOmega_z with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mPsaRange with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mAltitude with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mDvlAltitude with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mWaterSpeed with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mDvlValid with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mDvlNewData with 1702 elements.
Creating vector time with 1702 elements.
Creating vector mDeltaT with 1702 elements.
Creating vector time with 1702 elements.
Creating vector nfix with 1702 elements.
Creating vector time with 1702 elements.
Creating vector efix with 1702 elements.
Creating vector time with 1702 elements.
Creating vector filter_north with 1702 elements.
Creating vector time with 1702 elements.
Creating vector filter_east with 1702 elements.
Creating vector time with 1702 elements.
Creating vector filter_depth with 1702 elements.
Creating vector time with 1702 elements.
Creating vector north_current with 1702 elements.
Creating vector time with 1702 elements.
Creating vector east_current with 1702 elements.
Creating vector time with 1702 elements.
Creating vector speed_bias with 1702 elements.
Creating vector time with 1702 elements.
Creating vector heading_bias with 1702 elements.
Creating vector time with 1702 elements.
Creating vector latitude with 1702 elements.
Creating vector time with 1702 elements.
Creating vector longitude with 1702 elements.
Creating vector time with 1702 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/navigation.nc');
processNav(): median of positive valued depths = 3.2246
processNav(): Finding depths less than 22.5722 and times > 0
processNav(): length(Nav.depth) = 1702
processNav(): length(gindx)     = 1702
 
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/2010/2010258/2010.258.03/gps.nc')
Creating vector time with 298 elements.
Creating vector hours with 298 elements.
Creating vector time with 298 elements.
Creating vector minutes with 298 elements.
Creating vector time with 298 elements.
Creating vector seconds with 298 elements.
Creating vector time with 298 elements.
Creating vector centiSeconds with 298 elements.
Creating vector time with 298 elements.
Creating vector latitude with 298 elements.
Creating vector time with 298 elements.
Creating vector longitude with 298 elements.
Creating vector time with 298 elements.
Creating vector quality with 298 elements.
Creating vector time with 298 elements.
Creating vector numberOfSatellites with 298 elements.
Creating vector time with 298 elements.
Creating vector hdop with 298 elements.
Creating vector time with 298 elements.
Creating vector antennaHeight with 298 elements.
Creating vector time with 298 elements.
Creating vector geoHeight with 298 elements.
Creating vector time with 298 elements.
Creating vector dgpsDataAge with 298 elements.
Creating vector time with 298 elements.
Creating vector dgpsRSID with 298 elements.
Creating vector time with 298 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/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/2010/2010258/2010.258.03/parosci.nc')
Creating vector time with 2855 elements.
Creating vector depth with 2855 elements.
Creating vector time with 2855 elements.
Creating vector temp with 2855 elements.
Creating vector time with 2855 elements.
Creating vector pressure with 2855 elements.
Creating vector time with 2855 elements.
Creating vector temp_period with 2855 elements.
Creating vector time with 2855 elements.
Creating vector pres_period with 2855 elements.
Creating vector time with 2855 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.17111 max(Depth.data) = 405.509
Found 5 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.17111 max(Depth.data) = 283.9458
 
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/2010/2010258/2010.258.03/hydroscatlog.nc')
Creating vector time with 1521 elements.
Creating vector Seconds with 1521 elements.
Creating vector time with 1521 elements.
Creating vector HundrethsOfSeconds with 1521 elements.
Creating vector time with 1521 elements.
Creating vector Snorm1 with 1521 elements.
Creating vector time with 1521 elements.
Creating vector Snorm2 with 1521 elements.
Creating vector time with 1521 elements.
Creating vector Snorm3 with 1521 elements.
Creating vector time with 1521 elements.
Creating vector Gain_Status_1 with 1521 elements.
Creating vector time with 1521 elements.
Creating vector Gain_Status_2 with 1521 elements.
Creating vector time with 1521 elements.
Creating vector Gain_Status_3 with 1521 elements.
Creating vector time with 1521 elements.
Creating vector RawDepthValue with 1521 elements.
Creating vector time with 1521 elements.
Creating vector RawTempValue with 1521 elements.
Creating vector time with 1521 elements.
Creating vector Temperature with 1521 elements.
Creating vector time with 1521 elements.
Creating vector ErrorValue with 1521 elements.
Creating vector time with 1521 elements.
Creating vector bb470 with 1521 elements.
Creating vector time with 1521 elements.
Creating vector bb676 with 1521 elements.
Creating vector time with 1521 elements.
Creating vector fl676u with 1521 elements.
Creating vector time with 1521 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/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/2010/2010258/2010.258.03/ctdDriver.nc')
Creating vector time with 1448 elements.
Creating vector conductivity with 1448 elements.
Creating vector time with 1448 elements.
Creating vector temperature with 1448 elements.
Creating vector time with 1448 elements.
Creating vector cond_frequency with 1448 elements.
Creating vector time with 1448 elements.
Creating vector temp_frequency with 1448 elements.
Creating vector time with 1448 elements.
Creating vector spare with 1448 elements.
Creating vector time with 1448 elements.
Creating vector humidity with 1448 elements.
Creating vector time with 1448 elements.
Creating vector flow1 with 1448 elements.
Creating vector time with 1448 elements.
Creating vector rhodamine with 1448 elements.
Creating vector time with 1448 elements.
Creating vector dissolvedO2 with 1448 elements.
Creating vector time with 1448 elements.
Creating vector salinity with 1448 elements.
Creating vector time with 1448 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/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/2010/2010258/2010.258.03/ctdDriver2.nc')
Creating vector time with 1445 elements.
Creating vector conductivity with 1445 elements.
Creating vector time with 1445 elements.
Creating vector temperature with 1445 elements.
Creating vector time with 1445 elements.
Creating vector cond_frequency with 1445 elements.
Creating vector time with 1445 elements.
Creating vector temp_frequency with 1445 elements.
Creating vector time with 1445 elements.
Creating vector flow2 with 1445 elements.
Creating vector time with 1445 elements.
Creating vector spare with 1445 elements.
Creating vector time with 1445 elements.
Creating vector salinity with 1445 elements.
Creating vector time with 1445 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/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/2010/2010258/2010.258.03/isuslog.nc')
Creating vector time with 245 elements.
Creating vector isusNitrate with 245 elements.
Creating vector time with 245 elements.
Creating vector isusTemp with 245 elements.
Creating vector time with 245 elements.
Creating vector isusQuality with 245 elements.
Creating vector time with 245 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/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/2010/2010258/2010.258.03/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (37 x 994) with 36778 elements.
Creating vector time with 37 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (37 x 994) with 36778 elements.
Creating vector time with 37 elements.
Creating vector bin with 994 elements.
Creating matrix countList (37 x 994) with 36778 elements.
Creating vector time with 37 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 37 elements.
Creating vector time with 37 elements.
Creating vector transCount with 37 elements.
Creating vector time with 37 elements.
Creating vector nonTransCount with 37 elements.
Creating vector time with 37 elements.
Creating vector ai_mean with 37 elements.
Creating vector time with 37 elements.
Creating vector ai_min with 37 elements.
Creating vector time with 37 elements.
Creating vector ai_max with 37 elements.
Creating vector time with 37 elements.
Creating vector ai_std with 37 elements.
Creating vector time with 37 elements.
Creating vector esd_mean with 37 elements.
Creating vector time with 37 elements.
Creating vector esd_min with 37 elements.
Creating vector time with 37 elements.
Creating vector esd_max with 37 elements.
Creating vector time with 37 elements.
Creating vector esd_std with 37 elements.
Creating vector time with 37 elements.
Creating vector countSum with 37 elements.
Creating vector time with 37 elements.
Creating vector snapshot with 37 elements.
Creating vector time with 37 elements.
Creating vector threshold with 37 elements.
Creating vector time with 37 elements.
Creating vector sampleCount with 37 elements.
Creating vector time with 37 elements.
Creating vector flowCount with 37 elements.
Creating vector time with 37 elements.
Creating vector flowTime with 37 elements.
Creating vector time with 37 elements.
Creating vector bufferStatus with 37 elements.
Creating vector time with 37 elements.
Creating vector laserLevel with 37 elements.
Creating vector time with 37 elements.
Creating vector counter with 37 elements.
Creating vector time with 37 elements.
Creating vector counterPeriod with 37 elements.
Creating vector time with 37 elements.
Creating vector laserControl with 37 elements.
Creating vector time with 37 elements.
Creating vector countUnknownFrameCharacter with 37 elements.
Creating vector time with 37 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 37 elements.
Creating vector time with 37 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 37 elements.
Creating vector time with 37 elements.
Creating vector flowSpeed with 37 elements.
Creating vector time with 37 elements.
Creating vector countShortLFrameError with 37 elements.
Creating vector time with 37 elements.
Creating vector countGarbledLFrame with 37 elements.
Creating vector time with 37 elements.
Creating vector cFrameEsecs with 37 elements.
Creating vector time with 37 elements.
Creating vector correctedSampleCountList with 37 elements.
Creating vector time with 37 elements.
Creating vector time with 37 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.03/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.03.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2010.258.04
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/
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/2010/2010258/2010.258.04/navigation.nc')
Creating vector time with 641 elements.
Creating vector mPos_x with 641 elements.
Creating vector time with 641 elements.
Creating vector mPos_y with 641 elements.
Creating vector time with 641 elements.
Creating vector mDepth with 641 elements.
Creating vector time with 641 elements.
Creating vector mGpsNorth with 641 elements.
Creating vector time with 641 elements.
Creating vector mGpsEast with 641 elements.
Creating vector time with 641 elements.
Creating vector mGpsValid with 641 elements.
Creating vector time with 641 elements.
Creating vector mPhi with 641 elements.
Creating vector time with 641 elements.
Creating vector mTheta with 641 elements.
Creating vector time with 641 elements.
Creating vector mPsi with 641 elements.
Creating vector time with 641 elements.
Creating vector mOmega_x with 641 elements.
Creating vector time with 641 elements.
Creating vector mOmega_y with 641 elements.
Creating vector time with 641 elements.
Creating vector mOmega_z with 641 elements.
Creating vector time with 641 elements.
Creating vector mPsaRange with 641 elements.
Creating vector time with 641 elements.
Creating vector mAltitude with 641 elements.
Creating vector time with 641 elements.
Creating vector mDvlAltitude with 641 elements.
Creating vector time with 641 elements.
Creating vector mWaterSpeed with 641 elements.
Creating vector time with 641 elements.
Creating vector mDvlValid with 641 elements.
Creating vector time with 641 elements.
Creating vector mDvlNewData with 641 elements.
Creating vector time with 641 elements.
Creating vector mDeltaT with 641 elements.
Creating vector time with 641 elements.
Creating vector nfix with 641 elements.
Creating vector time with 641 elements.
Creating vector efix with 641 elements.
Creating vector time with 641 elements.
Creating vector filter_north with 641 elements.
Creating vector time with 641 elements.
Creating vector filter_east with 641 elements.
Creating vector time with 641 elements.
Creating vector filter_depth with 641 elements.
Creating vector time with 641 elements.
Creating vector north_current with 641 elements.
Creating vector time with 641 elements.
Creating vector east_current with 641 elements.
Creating vector time with 641 elements.
Creating vector speed_bias with 641 elements.
Creating vector time with 641 elements.
Creating vector heading_bias with 641 elements.
Creating vector time with 641 elements.
Creating vector latitude with 641 elements.
Creating vector time with 641 elements.
Creating vector longitude with 641 elements.
Creating vector time with 641 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/navigation.nc');
processNav(): median of positive valued depths = 2.3661
processNav(): Finding depths less than 16.563 and times > 0
processNav(): length(Nav.depth) = 641
processNav(): length(gindx)     = 615
 
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/2010/2010258/2010.258.04/gps.nc')
Creating vector time with 131 elements.
Creating vector hours with 131 elements.
Creating vector time with 131 elements.
Creating vector minutes with 131 elements.
Creating vector time with 131 elements.
Creating vector seconds with 131 elements.
Creating vector time with 131 elements.
Creating vector centiSeconds with 131 elements.
Creating vector time with 131 elements.
Creating vector latitude with 131 elements.
Creating vector time with 131 elements.
Creating vector longitude with 131 elements.
Creating vector time with 131 elements.
Creating vector quality with 131 elements.
Creating vector time with 131 elements.
Creating vector numberOfSatellites with 131 elements.
Creating vector time with 131 elements.
Creating vector hdop with 131 elements.
Creating vector time with 131 elements.
Creating vector antennaHeight with 131 elements.
Creating vector time with 131 elements.
Creating vector geoHeight with 131 elements.
Creating vector time with 131 elements.
Creating vector dgpsDataAge with 131 elements.
Creating vector time with 131 elements.
Creating vector dgpsRSID with 131 elements.
Creating vector time with 131 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/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/2010/2010258/2010.258.04/parosci.nc')
Creating vector time with 1213 elements.
Creating vector depth with 1213 elements.
Creating vector time with 1213 elements.
Creating vector temp with 1213 elements.
Creating vector time with 1213 elements.
Creating vector pressure with 1213 elements.
Creating vector time with 1213 elements.
Creating vector temp_period with 1213 elements.
Creating vector time with 1213 elements.
Creating vector pres_period with 1213 elements.
Creating vector time with 1213 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.20837 max(Depth.data) = 220.1289
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.20837 max(Depth.data) = 220.1289
 
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/2010/2010258/2010.258.04/hydroscatlog.nc')
Creating vector time with 668 elements.
Creating vector Seconds with 668 elements.
Creating vector time with 668 elements.
Creating vector HundrethsOfSeconds with 668 elements.
Creating vector time with 668 elements.
Creating vector Snorm1 with 668 elements.
Creating vector time with 668 elements.
Creating vector Snorm2 with 668 elements.
Creating vector time with 668 elements.
Creating vector Snorm3 with 668 elements.
Creating vector time with 668 elements.
Creating vector Gain_Status_1 with 668 elements.
Creating vector time with 668 elements.
Creating vector Gain_Status_2 with 668 elements.
Creating vector time with 668 elements.
Creating vector Gain_Status_3 with 668 elements.
Creating vector time with 668 elements.
Creating vector RawDepthValue with 668 elements.
Creating vector time with 668 elements.
Creating vector RawTempValue with 668 elements.
Creating vector time with 668 elements.
Creating vector Temperature with 668 elements.
Creating vector time with 668 elements.
Creating vector ErrorValue with 668 elements.
Creating vector time with 668 elements.
Creating vector bb470 with 668 elements.
Creating vector time with 668 elements.
Creating vector bb676 with 668 elements.
Creating vector time with 668 elements.
Creating vector fl676u with 668 elements.
Creating vector time with 668 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/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/2010/2010258/2010.258.04/ctdDriver.nc')
Creating vector time with 594 elements.
Creating vector conductivity with 594 elements.
Creating vector time with 594 elements.
Creating vector temperature with 594 elements.
Creating vector time with 594 elements.
Creating vector cond_frequency with 594 elements.
Creating vector time with 594 elements.
Creating vector temp_frequency with 594 elements.
Creating vector time with 594 elements.
Creating vector spare with 594 elements.
Creating vector time with 594 elements.
Creating vector humidity with 594 elements.
Creating vector time with 594 elements.
Creating vector flow1 with 594 elements.
Creating vector time with 594 elements.
Creating vector rhodamine with 594 elements.
Creating vector time with 594 elements.
Creating vector dissolvedO2 with 594 elements.
Creating vector time with 594 elements.
Creating vector salinity with 594 elements.
Creating vector time with 594 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/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/2010/2010258/2010.258.04/ctdDriver2.nc')
Creating vector time with 595 elements.
Creating vector conductivity with 595 elements.
Creating vector time with 595 elements.
Creating vector temperature with 595 elements.
Creating vector time with 595 elements.
Creating vector cond_frequency with 595 elements.
Creating vector time with 595 elements.
Creating vector temp_frequency with 595 elements.
Creating vector time with 595 elements.
Creating vector flow2 with 595 elements.
Creating vector time with 595 elements.
Creating vector spare with 595 elements.
Creating vector time with 595 elements.
Creating vector salinity with 595 elements.
Creating vector time with 595 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/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/2010/2010258/2010.258.04/isuslog.nc')
Creating vector time with 77 elements.
Creating vector isusNitrate with 77 elements.
Creating vector time with 77 elements.
Creating vector isusTemp with 77 elements.
Creating vector time with 77 elements.
Creating vector isusQuality with 77 elements.
Creating vector time with 77 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/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/2010/2010258/2010.258.04/biolume.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/biolume.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/biolume.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/biolume.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


Could not read from biolume.nc returning NaNs for fields.
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (17 x 994) with 16898 elements.
Creating vector time with 17 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (17 x 994) with 16898 elements.
Creating vector time with 17 elements.
Creating vector bin with 994 elements.
Creating matrix countList (17 x 994) with 16898 elements.
Creating vector time with 17 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 17 elements.
Creating vector time with 17 elements.
Creating vector transCount with 17 elements.
Creating vector time with 17 elements.
Creating vector nonTransCount with 17 elements.
Creating vector time with 17 elements.
Creating vector ai_mean with 17 elements.
Creating vector time with 17 elements.
Creating vector ai_min with 17 elements.
Creating vector time with 17 elements.
Creating vector ai_max with 17 elements.
Creating vector time with 17 elements.
Creating vector ai_std with 17 elements.
Creating vector time with 17 elements.
Creating vector esd_mean with 17 elements.
Creating vector time with 17 elements.
Creating vector esd_min with 17 elements.
Creating vector time with 17 elements.
Creating vector esd_max with 17 elements.
Creating vector time with 17 elements.
Creating vector esd_std with 17 elements.
Creating vector time with 17 elements.
Creating vector countSum with 17 elements.
Creating vector time with 17 elements.
Creating vector snapshot with 17 elements.
Creating vector time with 17 elements.
Creating vector threshold with 17 elements.
Creating vector time with 17 elements.
Creating vector sampleCount with 17 elements.
Creating vector time with 17 elements.
Creating vector flowCount with 17 elements.
Creating vector time with 17 elements.
Creating vector flowTime with 17 elements.
Creating vector time with 17 elements.
Creating vector bufferStatus with 17 elements.
Creating vector time with 17 elements.
Creating vector laserLevel with 17 elements.
Creating vector time with 17 elements.
Creating vector counter with 17 elements.
Creating vector time with 17 elements.
Creating vector counterPeriod with 17 elements.
Creating vector time with 17 elements.
Creating vector laserControl with 17 elements.
Creating vector time with 17 elements.
Creating vector countUnknownFrameCharacter with 17 elements.
Creating vector time with 17 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 17 elements.
Creating vector time with 17 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 17 elements.
Creating vector time with 17 elements.
Creating vector flowSpeed with 17 elements.
Creating vector time with 17 elements.
Creating vector countShortLFrameError with 17 elements.
Creating vector time with 17 elements.
Creating vector countGarbledLFrame with 17 elements.
Creating vector time with 17 elements.
Creating vector cFrameEsecs with 17 elements.
Creating vector time with 17 elements.
Creating vector correctedSampleCountList with 17 elements.
Creating vector time with 17 elements.
Creating vector time with 17 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010258/2010.258.04/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.04.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_2010.257.01.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.257.02.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.257.10.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.257.11.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.00.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.01.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.02.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.03.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.04.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 17 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_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 = 126 Gridding with nix = 378, iZ = 210
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...
   bbp420
   bbp700
   fl700_uncorr
   N
   BL
Only one good point or fewer - NaNing the gBL array.
   BLflow
Only one good point or fewer - NaNing the gBLflow array.
   LOPC
     count
     transCount
     nonTransCount
     LCcount
 
Masking and filtering with median filter of size 5...
  cvarname = gT
  cvarname = gS
  cvarname = gO
  cvarname = gN
  cvarname = gF
  cvarname = gB420
  cvarname = gB700
  cvarname = gBL
No valid data for gBL
  cvarname = gBLflow
No valid data for gBLflow
  cvarname = gLOPCcount
  cvarname = gLOPCtransCount
  cvarname = gLOPCnonTransCount
  cvarname = gLOPCLCcount
Encountered 0 NaN values in array of lon that is 140209 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: Some input points were outside the grid domain(s).
grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447)
No depth array returned by grdtrack.  Perhaps grdtrack could not be found in the search path.
Setting ocean depths to 4000m for the track.
Executing: /bin/rm -f ../results/2010257_GulperTimes.txt && touch ../results/2010257_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/2010/2010257/2010.257.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010257/2010.257.01/syslog -startEsecs 1284538774.4843 -surveyName Dorado389_2010_257_01_258_04 >> ../results/2010257_GulperTimes.txt
Executing: removeGulpDups.py ../results/2010257_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/2010/2010257/2010.257.02/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010257/2010.257.02/syslog -startEsecs 1284538774.4843 -surveyName Dorado389_2010_257_01_258_04 >> ../results/2010257_GulperTimes.txt
Executing: removeGulpDups.py ../results/2010257_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/2010/2010257/2010.257.10/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010257/2010.257.10/syslog -startEsecs 1284538774.4843 -surveyName Dorado389_2010_257_01_258_04 >> ../results/2010257_GulperTimes.txt
Executing: removeGulpDups.py ../results/2010257_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/2010/2010257/2010.257.11/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010257/2010.257.11/syslog -startEsecs 1284538774.4843 -surveyName Dorado389_2010_257_01_258_04 >> ../results/2010257_GulperTimes.txt
Executing: removeGulpDups.py ../results/2010257_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/2010/2010258/2010.258.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010258/2010.258.00/syslog -startEsecs 1284538774.4843 -surveyName Dorado389_2010_257_01_258_04 >> ../results/2010257_GulperTimes.txt
Executing: removeGulpDups.py ../results/2010257_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/2010/2010258/2010.258.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010258/2010.258.01/syslog -startEsecs 1284538774.4843 -surveyName Dorado389_2010_257_01_258_04 >> ../results/2010257_GulperTimes.txt
Executing: removeGulpDups.py ../results/2010257_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/2010/2010258/2010.258.02/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010258/2010.258.02/syslog -startEsecs 1284538774.4843 -surveyName Dorado389_2010_257_01_258_04 >> ../results/2010257_GulperTimes.txt
Executing: removeGulpDups.py ../results/2010257_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/2010/2010258/2010.258.03/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010258/2010.258.03/syslog -startEsecs 1284538774.4843 -surveyName Dorado389_2010_257_01_258_04 >> ../results/2010257_GulperTimes.txt
Executing: removeGulpDups.py ../results/2010257_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/2010/2010258/2010.258.04/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010258/2010.258.04/syslog -startEsecs 1284538774.4843 -surveyName Dorado389_2010_257_01_258_04 >> ../results/2010257_GulperTimes.txt
Executing: removeGulpDups.py ../results/2010257_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_gridded.mat

outvarstr =

    'gF gT gN gS gD gO gB420 gB700 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth '

2Column contouring gridded variable gD
2Column contouring gridded variable gT
2Column contouring gridded variable gS
2Column contouring gridded variable gN
2Column contouring gridded variable gO
2Column contouring gridded variable gB420
2Column contouring gridded variable gB700
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_2column.png
Elapsed time to save image: 6 seconds
Biolume contouring gridded variable gD
Biolume contouring gridded variable gT
Biolume contouring gridded variable gS
Biolume contouring gridded variable gN
Biolume contouring gridded variable gO
Biolume contouring gridded variable gB420
Biolume contouring gridded variable gB700
Biolume contouring gridded variable gF
Biolume contouring gridded variable gBL
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_biolume.png
Elapsed time to save image: 32 seconds
2Column contouring gridded variable gLOPCcount
2Column contouring gridded variable gLOPCtransCount
2Column contouring gridded variable gLOPCnonTransCount
2Column contouring gridded variable gLOPCLCcount
2Column contouring gridded variable gT
2Column contouring gridded variable gB420
2Column contouring gridded variable gB700
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_lopc.png
Elapsed time to save image: 8 seconds
 
 
*************************************************************************
Calling plot_survey_stats to produce histogram and profile statistics plots...
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_2column.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_biolume.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_lopc.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2010/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2010/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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Temperature.kml (deflated 95%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Salinity.kml (deflated 95%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Nitrate.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Oxygen.kml (deflated 95%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @420 nm', jetplus, varlimits(5,:), hs2.bbp420, time.hs2, auvnav, depth.hs2, resultspath);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Optical_Backscatter_420_nm.kml (deflated 95%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @700 nm', jetplus, varlimits(6,:), hs2.bbp700, time.hs2, auvnav, depth.hs2, resultspath);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Optical_Backscatter_700_nm.kml (deflated 95%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Chlorophyll_Fluorescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2010/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);
updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_04_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2010_257_01_258_04.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04.kml...
Copied to /mbari/AUVCTD/surveys/2010/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_257_01_258_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_2010_257_01_258_04.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
8 NaNs found in bbpRed.  Interpolating anyway.
1 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 78 NaN values in array of lon that is 21825 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: Some input points were outside the grid domain(s).
grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447)
No depth array returned by grdtrack.  Setting bottom depth to 1000 m
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04.txt...
Copied to /mbari/AUVCTD/surveys/2010/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_Gulper.txt...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2010/odv/
cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
8 NaNs found in bbpRed.  Interpolating anyway.
1 NaNs found in flRed_uncorr.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_decim.nc...
Copied to /mbari/AUVCTD/surveys/2010/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_2010_257_01_258_04.nc...
Copied to /mbari/AUVCTD/surveys/2010/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2010/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_257_01_258_04.mat...
Copied to /mbari/AUVCTD/surveys/2010/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2010_257_01_258_04 processed" mccann@mbari.org < mail_Dorado389_2010_257_01_258_04.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.257.01.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.257.02.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.257.10.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.257.11.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.00.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.01.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.02.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.03.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.258.04.mat
Processing time: 279 seconds