Execution of AUVprocess_main version 1.86 at 2018-06-01T21:50:27Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2004, ['315.00';'315.01';'315.02'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1')
 
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Processing data from SSDS via DODS server
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Processing AUV mission: 2004.315.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/
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/2004/2004315/2004.315.00/navigation.nc')
Creating vector time with 14309 elements.
Creating vector mPos_x with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mPos_y with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mDepth with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mGpsNorth with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mGpsEast with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mGpsValid with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mPhi with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mTheta with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mPsi with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mOmega_x with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mOmega_y with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mOmega_z with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mPsaRange with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mAltitude with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mWaterSpeed with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mDvlValid with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mDvlNewData with 14309 elements.
Creating vector time with 14309 elements.
Creating vector mDeltaT with 14309 elements.
Creating vector time with 14309 elements.
Creating vector latitude with 14309 elements.
Creating vector time with 14309 elements.
Creating vector longitude with 14309 elements.
Creating vector time with 14309 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/navigation.nc');
processNav(): median of positive valued depths = 6.9696
processNav(): Finding depths less than 48.7874 and times > 0
processNav(): length(Nav.depth) = 14309
processNav(): length(gindx)     = 14309
 
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/2004/2004315/2004.315.00/gps.nc')
Creating vector time with 597 elements.
Creating vector hours with 597 elements.
Creating vector time with 597 elements.
Creating vector minutes with 597 elements.
Creating vector time with 597 elements.
Creating vector seconds with 597 elements.
Creating vector time with 597 elements.
Creating vector centiSeconds with 597 elements.
Creating vector time with 597 elements.
Creating vector latitude with 597 elements.
Creating vector time with 597 elements.
Creating vector longitude with 597 elements.
Creating vector time with 597 elements.
Creating vector quality with 597 elements.
Creating vector time with 597 elements.
Creating vector numberOfSatellites with 597 elements.
Creating vector time with 597 elements.
Creating vector hdop with 597 elements.
Creating vector time with 597 elements.
Creating vector antennaHeight with 597 elements.
Creating vector time with 597 elements.
Creating vector geoHeight with 597 elements.
Creating vector time with 597 elements.
Creating vector dgpsDataAge with 597 elements.
Creating vector time with 597 elements.
Creating vector dgpsRSID with 597 elements.
Creating vector time with 597 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/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/2004/2004315/2004.315.00/parosci.nc')
Creating vector time with 14417 elements.
Creating vector depth with 14417 elements.
Creating vector time with 14417 elements.
Creating vector temp with 14417 elements.
Creating vector time with 14417 elements.
Creating vector pressure with 14417 elements.
Creating vector time with 14417 elements.
Creating vector temp_period with 14417 elements.
Creating vector time with 14417 elements.
Creating vector pres_period with 14417 elements.
Creating vector time with 14417 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.1473 max(Depth.data) = 15.726
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.1473 max(Depth.data) = 15.726
 
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/2004/2004315/2004.315.00/hydroscatlog.nc')
Creating vector time with 11514 elements.
Creating vector Seconds with 11514 elements.
Creating vector time with 11514 elements.
Creating vector HundrethsOfSeconds with 11514 elements.
Creating vector time with 11514 elements.
Creating vector Snorm1 with 11514 elements.
Creating vector time with 11514 elements.
Creating vector Snorm2 with 11514 elements.
Creating vector time with 11514 elements.
Creating vector Snorm3 with 11514 elements.
Creating vector time with 11514 elements.
Creating vector Gain_Status_1 with 11514 elements.
Creating vector time with 11514 elements.
Creating vector Gain_Status_2 with 11514 elements.
Creating vector time with 11514 elements.
Creating vector Gain_Status_3 with 11514 elements.
Creating vector time with 11514 elements.
Creating vector RawDepthValue with 11514 elements.
Creating vector time with 11514 elements.
Creating vector RawTempValue with 11514 elements.
Creating vector time with 11514 elements.
Creating vector Temperature with 11514 elements.
Creating vector time with 11514 elements.
Creating vector ErrorValue with 11514 elements.
Creating vector time with 11514 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/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/2004/2004315/2004.315.00/ctdDriver.nc')
Creating vector time with 11457 elements.
Creating vector conductivity with 11457 elements.
Creating vector time with 11457 elements.
Creating vector temperature with 11457 elements.
Creating vector time with 11457 elements.
Creating vector cond_frequency with 11457 elements.
Creating vector time with 11457 elements.
Creating vector temp_frequency with 11457 elements.
Creating vector time with 11457 elements.
Creating vector spare with 11457 elements.
Creating vector time with 11457 elements.
Creating vector humidity with 11457 elements.
Creating vector time with 11457 elements.
Creating vector flow1 with 11457 elements.
Creating vector time with 11457 elements.
Creating vector OBS with 11457 elements.
Creating vector time with 11457 elements.
Creating vector dissolvedO2 with 11457 elements.
Creating vector time with 11457 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/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/2004/2004315/2004.315.00/ctdDriver2.nc')
Creating vector time with 11458 elements.
Creating vector conductivity with 11458 elements.
Creating vector time with 11458 elements.
Creating vector temperature with 11458 elements.
Creating vector time with 11458 elements.
Creating vector cond_frequency with 11458 elements.
Creating vector time with 11458 elements.
Creating vector temp_frequency with 11458 elements.
Creating vector time with 11458 elements.
Creating vector flow2 with 11458 elements.
Creating vector time with 11458 elements.
Creating vector spare with 11458 elements.
Creating vector time with 11458 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/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/2004/2004315/2004.315.00/isuslog.nc')
Creating vector time with 1812 elements.
Creating vector isusNitrate with 1812 elements.
Creating vector time with 1812 elements.
Creating vector isusTemp with 1812 elements.
Creating vector time with 1812 elements.
Creating vector isusQuality with 1812 elements.
Creating vector time with 1812 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/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/2004/2004315/2004.315.00/biolume.nc')
Creating vector time with 2885 elements.
Creating vector rrr with 2885 elements.
Creating vector time with 2885 elements.
Creating vector cal_striing with 2885 elements.
Creating vector time with 2885 elements.
Creating vector pump with 2885 elements.
Creating vector time with 2885 elements.
Creating vector flow with 2885 elements.
Creating vector time with 2885 elements.
Creating vector humidity with 2885 elements.
Creating vector time with 2885 elements.
Creating vector temperature with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_0 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_1 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_2 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_3 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_4 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_5 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_6 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_7 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_8 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_9 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_10 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_11 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_12 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_13 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_14 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_15 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_16 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_17 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_18 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_19 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_20 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_21 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_22 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_23 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_24 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_25 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_26 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_27 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_28 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_29 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_30 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_31 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_32 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_33 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_34 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_35 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_36 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_37 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_38 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_39 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_40 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_41 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_42 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_43 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_44 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_45 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_46 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_47 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_48 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_49 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_50 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_51 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_52 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_53 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_54 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_55 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_56 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_57 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_58 with 2885 elements.
Creating vector time with 2885 elements.
Creating vector raw_59 with 2885 elements.
Creating vector time with 2885 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/lopc.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/lopc.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/lopc.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.00/lopc.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


*** Setting lopc structure to NaNs. *** 
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.315.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
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Processing AUV mission: 2004.315.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/
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/2004/2004315/2004.315.01/navigation.nc')
Creating vector time with 61921 elements.
Creating vector mPos_x with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mPos_y with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mDepth with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mGpsNorth with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mGpsEast with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mGpsValid with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mPhi with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mTheta with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mPsi with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mOmega_x with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mOmega_y with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mOmega_z with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mPsaRange with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mAltitude with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mWaterSpeed with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mDvlValid with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mDvlNewData with 61921 elements.
Creating vector time with 61921 elements.
Creating vector mDeltaT with 61921 elements.
Creating vector time with 61921 elements.
Creating vector latitude with 61921 elements.
Creating vector time with 61921 elements.
Creating vector longitude with 61921 elements.
Creating vector time with 61921 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/navigation.nc');
processNav(): median of positive valued depths = 7.6218
processNav(): Finding depths less than 53.3526 and times > 0
processNav(): length(Nav.depth) = 61921
processNav(): length(gindx)     = 61921
 
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/2004/2004315/2004.315.01/gps.nc')
Creating vector time with 772 elements.
Creating vector hours with 772 elements.
Creating vector time with 772 elements.
Creating vector minutes with 772 elements.
Creating vector time with 772 elements.
Creating vector seconds with 772 elements.
Creating vector time with 772 elements.
Creating vector centiSeconds with 772 elements.
Creating vector time with 772 elements.
Creating vector latitude with 772 elements.
Creating vector time with 772 elements.
Creating vector longitude with 772 elements.
Creating vector time with 772 elements.
Creating vector quality with 772 elements.
Creating vector time with 772 elements.
Creating vector numberOfSatellites with 772 elements.
Creating vector time with 772 elements.
Creating vector hdop with 772 elements.
Creating vector time with 772 elements.
Creating vector antennaHeight with 772 elements.
Creating vector time with 772 elements.
Creating vector geoHeight with 772 elements.
Creating vector time with 772 elements.
Creating vector dgpsDataAge with 772 elements.
Creating vector time with 772 elements.
Creating vector dgpsRSID with 772 elements.
Creating vector time with 772 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/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/2004/2004315/2004.315.01/parosci.nc')
Creating vector time with 61997 elements.
Creating vector depth with 61997 elements.
Creating vector time with 61997 elements.
Creating vector temp with 61997 elements.
Creating vector time with 61997 elements.
Creating vector pressure with 61997 elements.
Creating vector time with 61997 elements.
Creating vector temp_period with 61997 elements.
Creating vector time with 61997 elements.
Creating vector pres_period with 61997 elements.
Creating vector time with 61997 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.20516 max(Depth.data) = 16.9836
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.20516 max(Depth.data) = 16.9836
 
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/2004/2004315/2004.315.01/hydroscatlog.nc')
Creating vector time with 49583 elements.
Creating vector Seconds with 49583 elements.
Creating vector time with 49583 elements.
Creating vector HundrethsOfSeconds with 49583 elements.
Creating vector time with 49583 elements.
Creating vector Snorm1 with 49583 elements.
Creating vector time with 49583 elements.
Creating vector Snorm2 with 49583 elements.
Creating vector time with 49583 elements.
Creating vector Snorm3 with 49583 elements.
Creating vector time with 49583 elements.
Creating vector Gain_Status_1 with 49583 elements.
Creating vector time with 49583 elements.
Creating vector Gain_Status_2 with 49583 elements.
Creating vector time with 49583 elements.
Creating vector Gain_Status_3 with 49583 elements.
Creating vector time with 49583 elements.
Creating vector RawDepthValue with 49583 elements.
Creating vector time with 49583 elements.
Creating vector RawTempValue with 49583 elements.
Creating vector time with 49583 elements.
Creating vector Temperature with 49583 elements.
Creating vector time with 49583 elements.
Creating vector ErrorValue with 49583 elements.
Creating vector time with 49583 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/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/2004/2004315/2004.315.01/ctdDriver.nc')
Creating vector time with 49576 elements.
Creating vector conductivity with 49576 elements.
Creating vector time with 49576 elements.
Creating vector temperature with 49576 elements.
Creating vector time with 49576 elements.
Creating vector cond_frequency with 49576 elements.
Creating vector time with 49576 elements.
Creating vector temp_frequency with 49576 elements.
Creating vector time with 49576 elements.
Creating vector spare with 49576 elements.
Creating vector time with 49576 elements.
Creating vector humidity with 49576 elements.
Creating vector time with 49576 elements.
Creating vector flow1 with 49576 elements.
Creating vector time with 49576 elements.
Creating vector OBS with 49576 elements.
Creating vector time with 49576 elements.
Creating vector dissolvedO2 with 49576 elements.
Creating vector time with 49576 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/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/2004/2004315/2004.315.01/ctdDriver2.nc')
Creating vector time with 49574 elements.
Creating vector conductivity with 49574 elements.
Creating vector time with 49574 elements.
Creating vector temperature with 49574 elements.
Creating vector time with 49574 elements.
Creating vector cond_frequency with 49574 elements.
Creating vector time with 49574 elements.
Creating vector temp_frequency with 49574 elements.
Creating vector time with 49574 elements.
Creating vector flow2 with 49574 elements.
Creating vector time with 49574 elements.
Creating vector spare with 49574 elements.
Creating vector time with 49574 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/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/2004/2004315/2004.315.01/isuslog.nc')
Creating vector time with 7968 elements.
Creating vector isusNitrate with 7968 elements.
Creating vector time with 7968 elements.
Creating vector isusTemp with 7968 elements.
Creating vector time with 7968 elements.
Creating vector isusQuality with 7968 elements.
Creating vector time with 7968 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/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/2004/2004315/2004.315.01/biolume.nc')
Creating vector time with 12420 elements.
Creating vector rrr with 12420 elements.
Creating vector time with 12420 elements.
Creating vector cal_striing with 12420 elements.
Creating vector time with 12420 elements.
Creating vector pump with 12420 elements.
Creating vector time with 12420 elements.
Creating vector flow with 12420 elements.
Creating vector time with 12420 elements.
Creating vector humidity with 12420 elements.
Creating vector time with 12420 elements.
Creating vector temperature with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_0 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_1 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_2 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_3 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_4 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_5 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_6 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_7 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_8 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_9 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_10 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_11 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_12 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_13 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_14 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_15 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_16 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_17 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_18 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_19 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_20 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_21 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_22 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_23 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_24 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_25 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_26 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_27 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_28 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_29 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_30 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_31 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_32 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_33 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_34 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_35 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_36 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_37 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_38 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_39 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_40 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_41 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_42 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_43 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_44 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_45 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_46 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_47 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_48 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_49 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_50 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_51 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_52 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_53 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_54 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_55 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_56 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_57 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_58 with 12420 elements.
Creating vector time with 12420 elements.
Creating vector raw_59 with 12420 elements.
Creating vector time with 12420 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/lopc.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/lopc.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/lopc.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.01/lopc.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


*** Setting lopc structure to NaNs. *** 
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.315.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2004.315.02
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/
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/2004/2004315/2004.315.02/navigation.nc')
Creating vector time with 16952 elements.
Creating vector mPos_x with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mPos_y with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mDepth with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mGpsNorth with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mGpsEast with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mGpsValid with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mPhi with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mTheta with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mPsi with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mOmega_x with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mOmega_y with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mOmega_z with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mPsaRange with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mAltitude with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mWaterSpeed with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mDvlValid with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mDvlNewData with 16952 elements.
Creating vector time with 16952 elements.
Creating vector mDeltaT with 16952 elements.
Creating vector time with 16952 elements.
Creating vector latitude with 16952 elements.
Creating vector time with 16952 elements.
Creating vector longitude with 16952 elements.
Creating vector time with 16952 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/navigation.nc');
processNav(): median of positive valued depths = 7.9357
processNav(): Finding depths less than 55.5501 and times > 0
processNav(): length(Nav.depth) = 16952
processNav(): length(gindx)     = 16952
 
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/2004/2004315/2004.315.02/gps.nc')
Creating vector time with 232 elements.
Creating vector hours with 232 elements.
Creating vector time with 232 elements.
Creating vector minutes with 232 elements.
Creating vector time with 232 elements.
Creating vector seconds with 232 elements.
Creating vector time with 232 elements.
Creating vector centiSeconds with 232 elements.
Creating vector time with 232 elements.
Creating vector latitude with 232 elements.
Creating vector time with 232 elements.
Creating vector longitude with 232 elements.
Creating vector time with 232 elements.
Creating vector quality with 232 elements.
Creating vector time with 232 elements.
Creating vector numberOfSatellites with 232 elements.
Creating vector time with 232 elements.
Creating vector hdop with 232 elements.
Creating vector time with 232 elements.
Creating vector antennaHeight with 232 elements.
Creating vector time with 232 elements.
Creating vector geoHeight with 232 elements.
Creating vector time with 232 elements.
Creating vector dgpsDataAge with 232 elements.
Creating vector time with 232 elements.
Creating vector dgpsRSID with 232 elements.
Creating vector time with 232 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/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/2004/2004315/2004.315.02/parosci.nc')
Creating vector time with 17053 elements.
Creating vector depth with 17053 elements.
Creating vector time with 17053 elements.
Creating vector temp with 17053 elements.
Creating vector time with 17053 elements.
Creating vector pressure with 17053 elements.
Creating vector time with 17053 elements.
Creating vector temp_period with 17053 elements.
Creating vector time with 17053 elements.
Creating vector pres_period with 17053 elements.
Creating vector time with 17053 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.17908 max(Depth.data) = 15.8511
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.17908 max(Depth.data) = 15.8511
 
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/2004/2004315/2004.315.02/hydroscatlog.nc')
Creating vector time with 13621 elements.
Creating vector Seconds with 13621 elements.
Creating vector time with 13621 elements.
Creating vector HundrethsOfSeconds with 13621 elements.
Creating vector time with 13621 elements.
Creating vector Snorm1 with 13621 elements.
Creating vector time with 13621 elements.
Creating vector Snorm2 with 13621 elements.
Creating vector time with 13621 elements.
Creating vector Snorm3 with 13621 elements.
Creating vector time with 13621 elements.
Creating vector Gain_Status_1 with 13621 elements.
Creating vector time with 13621 elements.
Creating vector Gain_Status_2 with 13621 elements.
Creating vector time with 13621 elements.
Creating vector Gain_Status_3 with 13621 elements.
Creating vector time with 13621 elements.
Creating vector RawDepthValue with 13621 elements.
Creating vector time with 13621 elements.
Creating vector RawTempValue with 13621 elements.
Creating vector time with 13621 elements.
Creating vector Temperature with 13621 elements.
Creating vector time with 13621 elements.
Creating vector ErrorValue with 13621 elements.
Creating vector time with 13621 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/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/2004/2004315/2004.315.02/ctdDriver.nc')
Creating vector time with 13599 elements.
Creating vector conductivity with 13599 elements.
Creating vector time with 13599 elements.
Creating vector temperature with 13599 elements.
Creating vector time with 13599 elements.
Creating vector cond_frequency with 13599 elements.
Creating vector time with 13599 elements.
Creating vector temp_frequency with 13599 elements.
Creating vector time with 13599 elements.
Creating vector spare with 13599 elements.
Creating vector time with 13599 elements.
Creating vector humidity with 13599 elements.
Creating vector time with 13599 elements.
Creating vector flow1 with 13599 elements.
Creating vector time with 13599 elements.
Creating vector OBS with 13599 elements.
Creating vector time with 13599 elements.
Creating vector dissolvedO2 with 13599 elements.
Creating vector time with 13599 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/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/2004/2004315/2004.315.02/ctdDriver2.nc')
Creating vector time with 13600 elements.
Creating vector conductivity with 13600 elements.
Creating vector time with 13600 elements.
Creating vector temperature with 13600 elements.
Creating vector time with 13600 elements.
Creating vector cond_frequency with 13600 elements.
Creating vector time with 13600 elements.
Creating vector temp_frequency with 13600 elements.
Creating vector time with 13600 elements.
Creating vector flow2 with 13600 elements.
Creating vector time with 13600 elements.
Creating vector spare with 13600 elements.
Creating vector time with 13600 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/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/2004/2004315/2004.315.02/isuslog.nc')
Creating vector time with 2183 elements.
Creating vector isusNitrate with 2183 elements.
Creating vector time with 2183 elements.
Creating vector isusTemp with 2183 elements.
Creating vector time with 2183 elements.
Creating vector isusQuality with 2183 elements.
Creating vector time with 2183 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/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/2004/2004315/2004.315.02/biolume.nc')
Creating vector time with 3426 elements.
Creating vector rrr with 3426 elements.
Creating vector time with 3426 elements.
Creating vector cal_striing with 3426 elements.
Creating vector time with 3426 elements.
Creating vector pump with 3426 elements.
Creating vector time with 3426 elements.
Creating vector flow with 3426 elements.
Creating vector time with 3426 elements.
Creating vector humidity with 3426 elements.
Creating vector time with 3426 elements.
Creating vector temperature with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_0 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_1 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_2 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_3 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_4 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_5 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_6 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_7 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_8 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_9 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_10 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_11 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_12 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_13 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_14 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_15 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_16 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_17 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_18 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_19 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_20 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_21 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_22 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_23 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_24 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_25 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_26 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_27 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_28 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_29 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_30 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_31 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_32 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_33 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_34 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_35 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_36 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_37 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_38 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_39 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_40 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_41 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_42 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_43 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_44 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_45 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_46 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_47 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_48 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_49 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_50 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_51 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_52 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_53 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_54 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_55 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_56 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_57 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_58 with 3426 elements.
Creating vector time with 3426 elements.
Creating vector raw_59 with 3426 elements.
Creating vector time with 3426 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/lopc.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/lopc.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/lopc.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004315/2004.315.02/lopc.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


*** Setting lopc structure to NaNs. *** 
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.315.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Calling build_auv_survey.m to construct survey file...

SecondaryDissolvedO2 =

     []

Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.315.00.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.315.01.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.315.02.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 11 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02.mat
 
 
*************************************************************************
Calling plot_sections from ../viz to produce section plots ...
Using median boxcar filter of vector...
Using mean boxcar filter of vector...
Number of profiles found = 164 Gridding with nix = 492, iZ = 31
Using mean boxcar filter of vector...
Using mean boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Gridding...
   T
   S
   O
Using median boxcar filter of vector...
Using median boxcar filter of vector...
Using median boxcar filter of vector...
   bbp470
   bbp676
   fl676_uncorr
   N
   BL
   BLflow
   LOPC
Only one good point or fewer - NaNing the gLOPCcount array.
                             - NaNing the gLOPCtransCount array.
                             - NaNing the gLOPCnonTransCount array.
                             - NaNing the gLOPCLCcount array.
 
Masking and filtering with median filter of size 5...
  cvarname = gT
  cvarname = gS
  cvarname = gO
  cvarname = gN
  cvarname = gF
  cvarname = gB470
  cvarname = gB676
  cvarname = gBL
  cvarname = gBLflow
  cvarname = gLOPCcount
No valid data for gLOPCcount
  cvarname = gLOPCtransCount
No valid data for gLOPCtransCount
  cvarname = gLOPCnonTransCount
No valid data for gLOPCnonTransCount
  cvarname = gLOPCLCcount
No valid data for gLOPCLCcount
Encountered 0 NaN values in array of lon that is 93107 elements long
! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath
grdtrack: Warning: -b option with type s, S, or D are deprecated; Use <n>f or <n>d, with w to indicate swab
grdtrack: Processing input grid(s)
grdtrack: Output 1 columns via binary records using format f
grdtrack: Sampled 93107 points from grid Monterey25.grd (2876 x 2447)
Getting short wave radiation data from M1 for little plot above the biolume section plot
Creating vector TIME with 119091 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 11/10/2004 07:30  to 11/10/2004 14:30 

swr =

   23.2123
  114.2734
  212.1307
  195.0826
   71.7834
  113.7306
  148.9180
   81.4329

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2004315_GulperTimes.txt && touch ../results/2004315_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/2004/2004315/2004.315.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004315/2004.315.00/syslog -startEsecs 1100121698.7604 -surveyName Dorado389_2004_315_00_315_02 >> ../results/2004315_GulperTimes.txt
Executing: removeGulpDups.py ../results/2004315_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/2004/2004315/2004.315.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004315/2004.315.01/syslog -startEsecs 1100121698.7604 -surveyName Dorado389_2004_315_00_315_02 >> ../results/2004315_GulperTimes.txt
Executing: removeGulpDups.py ../results/2004315_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/2004/2004315/2004.315.02/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004315/2004.315.02/syslog -startEsecs 1100121698.7604 -surveyName Dorado389_2004_315_00_315_02 >> ../results/2004315_GulperTimes.txt
Executing: removeGulpDups.py ../results/2004315_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_gridded.mat

outvarstr =

    'gF gT gN gS gD gO gB470 gB676 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth '

2Column contouring gridded variable gD
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gT
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gS
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gN
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gO
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB470
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB676
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gF
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_2column.png
Elapsed time to save image: 7 seconds
Biolume contouring gridded variable gD
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gT
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gS
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gN
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gO
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gB470
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gB676
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gF
  Drawing bottom contour from EM300 data
Biolume contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_biolume.png
Elapsed time to save image: 27 seconds
2Column contouring gridded variable gLOPCcount
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gLOPCtransCount
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gLOPCnonTransCount
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gLOPCLCcount
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gT
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB470
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB676
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gF
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_lopc.png
Elapsed time to save image: 7 seconds
 
 
*************************************************************************
Calling plot_survey_stats to produce histogram and profile statistics plots...
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_2column.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_biolume.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_lopc.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2004/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing KML files ...
KML = write_kml(survey_shrt_filename_base, 'Temperature', jetplus, varlimits(1,:), ctd1.T, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Salinity.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @470 nm', jetplus, varlimits(5,:), hs2.bbp470, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Optical_Backscatter_470_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Optical_Backscatter_470_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Optical_Backscatter_676_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Optical_Backscatter_676_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2004/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);
Could not do interp1: The grid vectors must contain unique points.
Did not write KML for this variable.  Rethrowing error.
Could not create .kmz for Bioluminescence            
KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2004_315_00_315_02.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02.kml...
Copied to /mbari/AUVCTD/surveys/2004/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
[Warning: File
'/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_315_00_315_02_LOPC_Total_Count.kml'
not found.] 
[> In create_data_products (line 414)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpRed.  Interpolating anyway.
Encountered 10 NaN values in array of lon that is 11963 elements long
! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath
grdtrack: Warning: -b option with type s, S, or D are deprecated; Use <n>f or <n>d, with w to indicate swab
grdtrack: Processing input grid(s)
grdtrack: Output 1 columns via binary records using format f
grdtrack: Sampled 11953 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 11953 are not equal to number of Lat lon points = 11963
AUV track probably goes outside of the range of the .grd file being used.   Setting bottom depths to 1000 m
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02.txt...
Copied to /mbari/AUVCTD/surveys/2004/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_Gulper.txt...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2004/odv/
cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_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 bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_decim.nc...
Copied to /mbari/AUVCTD/surveys/2004/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_2004_315_00_315_02.nc...
Copied to /mbari/AUVCTD/surveys/2004/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2004/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_315_00_315_02.mat...
Copied to /mbari/AUVCTD/surveys/2004/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2004_315_00_315_02 processed" mccann@mbari.org < mail_Dorado389_2004_315_00_315_02.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.315.00.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.315.01.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.315.02.mat
Processing time: 110 seconds