Execution of AUVprocess_main version 1.86 at 2018-06-01T21:53:42Z on elvis
Matlab command executed: 
   AUVprocess_main('BIOLUME', 2004, ['317.00';'317.01';'317.02'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1')
 
*************************************************************************
Processing data from SSDS via DODS server
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2004.317.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/
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/2004/2004317/2004.317.00/navigation.nc')
Creating vector time with 7531 elements.
Creating vector mPos_x with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mPos_y with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mDepth with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mGpsNorth with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mGpsEast with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mGpsValid with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mPhi with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mTheta with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mPsi with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mOmega_x with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mOmega_y with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mOmega_z with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mPsaRange with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mAltitude with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mWaterSpeed with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mDvlValid with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mDvlNewData with 7531 elements.
Creating vector time with 7531 elements.
Creating vector mDeltaT with 7531 elements.
Creating vector time with 7531 elements.
Creating vector latitude with 7531 elements.
Creating vector time with 7531 elements.
Creating vector longitude with 7531 elements.
Creating vector time with 7531 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/navigation.nc');
processNav(): median of positive valued depths = 10.4969
processNav(): Finding depths less than 73.4786 and times > 0
processNav(): length(Nav.depth) = 7531
processNav(): length(gindx)     = 7531
 
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/2004/2004317/2004.317.00/gps.nc')
Creating vector time with 336 elements.
Creating vector hours with 336 elements.
Creating vector time with 336 elements.
Creating vector minutes with 336 elements.
Creating vector time with 336 elements.
Creating vector seconds with 336 elements.
Creating vector time with 336 elements.
Creating vector centiSeconds with 336 elements.
Creating vector time with 336 elements.
Creating vector latitude with 336 elements.
Creating vector time with 336 elements.
Creating vector longitude with 336 elements.
Creating vector time with 336 elements.
Creating vector quality with 336 elements.
Creating vector time with 336 elements.
Creating vector numberOfSatellites with 336 elements.
Creating vector time with 336 elements.
Creating vector hdop with 336 elements.
Creating vector time with 336 elements.
Creating vector antennaHeight with 336 elements.
Creating vector time with 336 elements.
Creating vector geoHeight with 336 elements.
Creating vector time with 336 elements.
Creating vector dgpsDataAge with 336 elements.
Creating vector time with 336 elements.
Creating vector dgpsRSID with 336 elements.
Creating vector time with 336 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/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/2004/2004317/2004.317.00/parosci.nc')
Creating vector time with 7635 elements.
Creating vector depth with 7635 elements.
Creating vector time with 7635 elements.
Creating vector temp with 7635 elements.
Creating vector time with 7635 elements.
Creating vector pressure with 7635 elements.
Creating vector time with 7635 elements.
Creating vector temp_period with 7635 elements.
Creating vector time with 7635 elements.
Creating vector pres_period with 7635 elements.
Creating vector time with 7635 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.13333 max(Depth.data) = 16.7304
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.13333 max(Depth.data) = 16.7304
 
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/2004/2004317/2004.317.00/hydroscatlog.nc')
Creating vector time with 6090 elements.
Creating vector Seconds with 6090 elements.
Creating vector time with 6090 elements.
Creating vector HundrethsOfSeconds with 6090 elements.
Creating vector time with 6090 elements.
Creating vector Snorm1 with 6090 elements.
Creating vector time with 6090 elements.
Creating vector Snorm2 with 6090 elements.
Creating vector time with 6090 elements.
Creating vector Snorm3 with 6090 elements.
Creating vector time with 6090 elements.
Creating vector Gain_Status_1 with 6090 elements.
Creating vector time with 6090 elements.
Creating vector Gain_Status_2 with 6090 elements.
Creating vector time with 6090 elements.
Creating vector Gain_Status_3 with 6090 elements.
Creating vector time with 6090 elements.
Creating vector RawDepthValue with 6090 elements.
Creating vector time with 6090 elements.
Creating vector RawTempValue with 6090 elements.
Creating vector time with 6090 elements.
Creating vector Temperature with 6090 elements.
Creating vector time with 6090 elements.
Creating vector ErrorValue with 6090 elements.
Creating vector time with 6090 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/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/2004/2004317/2004.317.00/ctdDriver.nc')
Creating vector time with 6033 elements.
Creating vector conductivity with 6033 elements.
Creating vector time with 6033 elements.
Creating vector temperature with 6033 elements.
Creating vector time with 6033 elements.
Creating vector cond_frequency with 6033 elements.
Creating vector time with 6033 elements.
Creating vector temp_frequency with 6033 elements.
Creating vector time with 6033 elements.
Creating vector spare with 6033 elements.
Creating vector time with 6033 elements.
Creating vector humidity with 6033 elements.
Creating vector time with 6033 elements.
Creating vector flow1 with 6033 elements.
Creating vector time with 6033 elements.
Creating vector OBS with 6033 elements.
Creating vector time with 6033 elements.
Creating vector dissolvedO2 with 6033 elements.
Creating vector time with 6033 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/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/2004/2004317/2004.317.00/ctdDriver2.nc')
Creating vector time with 6034 elements.
Creating vector conductivity with 6034 elements.
Creating vector time with 6034 elements.
Creating vector temperature with 6034 elements.
Creating vector time with 6034 elements.
Creating vector cond_frequency with 6034 elements.
Creating vector time with 6034 elements.
Creating vector temp_frequency with 6034 elements.
Creating vector time with 6034 elements.
Creating vector flow2 with 6034 elements.
Creating vector time with 6034 elements.
Creating vector spare with 6034 elements.
Creating vector time with 6034 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/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/2004/2004317/2004.317.00/isuslog.nc')
Creating vector time with 940 elements.
Creating vector isusNitrate with 940 elements.
Creating vector time with 940 elements.
Creating vector isusTemp with 940 elements.
Creating vector time with 940 elements.
Creating vector isusQuality with 940 elements.
Creating vector time with 940 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/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/2004/2004317/2004.317.00/biolume.nc')
Creating vector time with 1529 elements.
Creating vector rrr with 1529 elements.
Creating vector time with 1529 elements.
Creating vector cal_striing with 1529 elements.
Creating vector time with 1529 elements.
Creating vector pump with 1529 elements.
Creating vector time with 1529 elements.
Creating vector flow with 1529 elements.
Creating vector time with 1529 elements.
Creating vector humidity with 1529 elements.
Creating vector time with 1529 elements.
Creating vector temperature with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_0 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_1 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_2 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_3 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_4 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_5 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_6 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_7 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_8 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_9 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_10 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_11 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_12 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_13 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_14 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_15 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_16 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_17 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_18 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_19 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_20 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_21 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_22 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_23 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_24 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_25 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_26 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_27 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_28 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_29 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_30 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_31 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_32 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_33 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_34 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_35 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_36 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_37 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_38 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_39 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_40 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_41 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_42 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_43 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_44 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_45 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_46 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_47 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_48 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_49 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_50 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_51 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_52 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_53 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_54 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_55 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_56 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_57 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_58 with 1529 elements.
Creating vector time with 1529 elements.
Creating vector raw_59 with 1529 elements.
Creating vector time with 1529 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.00/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/2004/2004317/2004.317.00/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/2004/2004317/2004.317.00/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/2004/2004317/2004.317.00/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/2004/2004317/2004.317.00/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_2004.317.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2004.317.01
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/
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/2004/2004317/2004.317.01/navigation.nc')
Creating vector time with 98694 elements.
Creating vector mPos_x with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mPos_y with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mDepth with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mGpsNorth with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mGpsEast with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mGpsValid with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mPhi with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mTheta with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mPsi with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mOmega_x with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mOmega_y with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mOmega_z with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mPsaRange with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mAltitude with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mWaterSpeed with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mDvlValid with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mDvlNewData with 98694 elements.
Creating vector time with 98694 elements.
Creating vector mDeltaT with 98694 elements.
Creating vector time with 98694 elements.
Creating vector latitude with 98694 elements.
Creating vector time with 98694 elements.
Creating vector longitude with 98694 elements.
Creating vector time with 98694 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/navigation.nc');
processNav(): median of positive valued depths = 32.9998
processNav(): Finding depths less than 230.9984 and times > 0
processNav(): length(Nav.depth) = 98694
processNav(): length(gindx)     = 98694
 
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/2004/2004317/2004.317.01/gps.nc')
Creating vector time with 866 elements.
Creating vector hours with 866 elements.
Creating vector time with 866 elements.
Creating vector minutes with 866 elements.
Creating vector time with 866 elements.
Creating vector seconds with 866 elements.
Creating vector time with 866 elements.
Creating vector centiSeconds with 866 elements.
Creating vector time with 866 elements.
Creating vector latitude with 866 elements.
Creating vector time with 866 elements.
Creating vector longitude with 866 elements.
Creating vector time with 866 elements.
Creating vector quality with 866 elements.
Creating vector time with 866 elements.
Creating vector numberOfSatellites with 866 elements.
Creating vector time with 866 elements.
Creating vector hdop with 866 elements.
Creating vector time with 866 elements.
Creating vector antennaHeight with 866 elements.
Creating vector time with 866 elements.
Creating vector geoHeight with 866 elements.
Creating vector time with 866 elements.
Creating vector dgpsDataAge with 866 elements.
Creating vector time with 866 elements.
Creating vector dgpsRSID with 866 elements.
Creating vector time with 866 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/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/2004/2004317/2004.317.01/parosci.nc')
Creating vector time with 98803 elements.
Creating vector depth with 98803 elements.
Creating vector time with 98803 elements.
Creating vector temp with 98803 elements.
Creating vector time with 98803 elements.
Creating vector pressure with 98803 elements.
Creating vector time with 98803 elements.
Creating vector temp_period with 98803 elements.
Creating vector time with 98803 elements.
Creating vector pres_period with 98803 elements.
Creating vector time with 98803 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.29657 max(Depth.data) = 101.0537
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.29657 max(Depth.data) = 101.0537
 
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/2004/2004317/2004.317.01/hydroscatlog.nc')
Creating vector time with 78992 elements.
Creating vector Seconds with 78992 elements.
Creating vector time with 78992 elements.
Creating vector HundrethsOfSeconds with 78992 elements.
Creating vector time with 78992 elements.
Creating vector Snorm1 with 78992 elements.
Creating vector time with 78992 elements.
Creating vector Snorm2 with 78992 elements.
Creating vector time with 78992 elements.
Creating vector Snorm3 with 78992 elements.
Creating vector time with 78992 elements.
Creating vector Gain_Status_1 with 78992 elements.
Creating vector time with 78992 elements.
Creating vector Gain_Status_2 with 78992 elements.
Creating vector time with 78992 elements.
Creating vector Gain_Status_3 with 78992 elements.
Creating vector time with 78992 elements.
Creating vector RawDepthValue with 78992 elements.
Creating vector time with 78992 elements.
Creating vector RawTempValue with 78992 elements.
Creating vector time with 78992 elements.
Creating vector Temperature with 78992 elements.
Creating vector time with 78992 elements.
Creating vector ErrorValue with 78992 elements.
Creating vector time with 78992 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/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/2004/2004317/2004.317.01/ctdDriver.nc')
Creating vector time with 78968 elements.
Creating vector conductivity with 78968 elements.
Creating vector time with 78968 elements.
Creating vector temperature with 78968 elements.
Creating vector time with 78968 elements.
Creating vector cond_frequency with 78968 elements.
Creating vector time with 78968 elements.
Creating vector temp_frequency with 78968 elements.
Creating vector time with 78968 elements.
Creating vector spare with 78968 elements.
Creating vector time with 78968 elements.
Creating vector humidity with 78968 elements.
Creating vector time with 78968 elements.
Creating vector flow1 with 78968 elements.
Creating vector time with 78968 elements.
Creating vector OBS with 78968 elements.
Creating vector time with 78968 elements.
Creating vector dissolvedO2 with 78968 elements.
Creating vector time with 78968 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/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/2004/2004317/2004.317.01/ctdDriver2.nc')
Creating vector time with 78969 elements.
Creating vector conductivity with 78969 elements.
Creating vector time with 78969 elements.
Creating vector temperature with 78969 elements.
Creating vector time with 78969 elements.
Creating vector cond_frequency with 78969 elements.
Creating vector time with 78969 elements.
Creating vector temp_frequency with 78969 elements.
Creating vector time with 78969 elements.
Creating vector flow2 with 78969 elements.
Creating vector time with 78969 elements.
Creating vector spare with 78969 elements.
Creating vector time with 78969 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/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/2004/2004317/2004.317.01/isuslog.nc')
Creating vector time with 12738 elements.
Creating vector isusNitrate with 12738 elements.
Creating vector time with 12738 elements.
Creating vector isusTemp with 12738 elements.
Creating vector time with 12738 elements.
Creating vector isusQuality with 12738 elements.
Creating vector time with 12738 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/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/2004/2004317/2004.317.01/biolume.nc')
Creating vector time with 19764 elements.
Creating vector rrr with 19764 elements.
Creating vector time with 19764 elements.
Creating vector cal_striing with 19764 elements.
Creating vector time with 19764 elements.
Creating vector pump with 19764 elements.
Creating vector time with 19764 elements.
Creating vector flow with 19764 elements.
Creating vector time with 19764 elements.
Creating vector humidity with 19764 elements.
Creating vector time with 19764 elements.
Creating vector temperature with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_0 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_1 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_2 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_3 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_4 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_5 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_6 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_7 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_8 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_9 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_10 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_11 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_12 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_13 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_14 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_15 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_16 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_17 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_18 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_19 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_20 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_21 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_22 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_23 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_24 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_25 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_26 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_27 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_28 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_29 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_30 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_31 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_32 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_33 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_34 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_35 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_36 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_37 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_38 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_39 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_40 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_41 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_42 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_43 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_44 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_45 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_46 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_47 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_48 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_49 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_50 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_51 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_52 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_53 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_54 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_55 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_56 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_57 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_58 with 19764 elements.
Creating vector time with 19764 elements.
Creating vector raw_59 with 19764 elements.
Creating vector time with 19764 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.01/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/2004/2004317/2004.317.01/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/2004/2004317/2004.317.01/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/2004/2004317/2004.317.01/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/2004/2004317/2004.317.01/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_2004.317.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2004.317.02
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/
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/2004/2004317/2004.317.02/navigation.nc')
Creating vector time with 40104 elements.
Creating vector mPos_x with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mPos_y with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mDepth with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mGpsNorth with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mGpsEast with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mGpsValid with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mPhi with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mTheta with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mPsi with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mOmega_x with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mOmega_y with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mOmega_z with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mPsaRange with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mAltitude with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mWaterSpeed with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mDvlValid with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mDvlNewData with 40104 elements.
Creating vector time with 40104 elements.
Creating vector mDeltaT with 40104 elements.
Creating vector time with 40104 elements.
Creating vector latitude with 40104 elements.
Creating vector time with 40104 elements.
Creating vector longitude with 40104 elements.
Creating vector time with 40104 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/navigation.nc');
processNav(): median of positive valued depths = 43.5329
processNav(): Finding depths less than 304.7304 and times > 0
processNav(): length(Nav.depth) = 40104
processNav(): length(gindx)     = 40104
 
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/2004/2004317/2004.317.02/gps.nc')
Creating vector time with 293 elements.
Creating vector hours with 293 elements.
Creating vector time with 293 elements.
Creating vector minutes with 293 elements.
Creating vector time with 293 elements.
Creating vector seconds with 293 elements.
Creating vector time with 293 elements.
Creating vector centiSeconds with 293 elements.
Creating vector time with 293 elements.
Creating vector latitude with 293 elements.
Creating vector time with 293 elements.
Creating vector longitude with 293 elements.
Creating vector time with 293 elements.
Creating vector quality with 293 elements.
Creating vector time with 293 elements.
Creating vector numberOfSatellites with 293 elements.
Creating vector time with 293 elements.
Creating vector hdop with 293 elements.
Creating vector time with 293 elements.
Creating vector antennaHeight with 293 elements.
Creating vector time with 293 elements.
Creating vector geoHeight with 293 elements.
Creating vector time with 293 elements.
Creating vector dgpsDataAge with 293 elements.
Creating vector time with 293 elements.
Creating vector dgpsRSID with 293 elements.
Creating vector time with 293 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/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/2004/2004317/2004.317.02/parosci.nc')
Creating vector time with 40207 elements.
Creating vector depth with 40207 elements.
Creating vector time with 40207 elements.
Creating vector temp with 40207 elements.
Creating vector time with 40207 elements.
Creating vector pressure with 40207 elements.
Creating vector time with 40207 elements.
Creating vector temp_period with 40207 elements.
Creating vector time with 40207 elements.
Creating vector pres_period with 40207 elements.
Creating vector time with 40207 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.16444 max(Depth.data) = 98.9483
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.16444 max(Depth.data) = 98.9483
 
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/2004/2004317/2004.317.02/hydroscatlog.nc')
Creating vector time with 32137 elements.
Creating vector Seconds with 32137 elements.
Creating vector time with 32137 elements.
Creating vector HundrethsOfSeconds with 32137 elements.
Creating vector time with 32137 elements.
Creating vector Snorm1 with 32137 elements.
Creating vector time with 32137 elements.
Creating vector Snorm2 with 32137 elements.
Creating vector time with 32137 elements.
Creating vector Snorm3 with 32137 elements.
Creating vector time with 32137 elements.
Creating vector Gain_Status_1 with 32137 elements.
Creating vector time with 32137 elements.
Creating vector Gain_Status_2 with 32137 elements.
Creating vector time with 32137 elements.
Creating vector Gain_Status_3 with 32137 elements.
Creating vector time with 32137 elements.
Creating vector RawDepthValue with 32137 elements.
Creating vector time with 32137 elements.
Creating vector RawTempValue with 32137 elements.
Creating vector time with 32137 elements.
Creating vector Temperature with 32137 elements.
Creating vector time with 32137 elements.
Creating vector ErrorValue with 32137 elements.
Creating vector time with 32137 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/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/2004/2004317/2004.317.02/ctdDriver.nc')
Creating vector time with 32089 elements.
Creating vector conductivity with 32089 elements.
Creating vector time with 32089 elements.
Creating vector temperature with 32089 elements.
Creating vector time with 32089 elements.
Creating vector cond_frequency with 32089 elements.
Creating vector time with 32089 elements.
Creating vector temp_frequency with 32089 elements.
Creating vector time with 32089 elements.
Creating vector spare with 32089 elements.
Creating vector time with 32089 elements.
Creating vector humidity with 32089 elements.
Creating vector time with 32089 elements.
Creating vector flow1 with 32089 elements.
Creating vector time with 32089 elements.
Creating vector OBS with 32089 elements.
Creating vector time with 32089 elements.
Creating vector dissolvedO2 with 32089 elements.
Creating vector time with 32089 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/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/2004/2004317/2004.317.02/ctdDriver2.nc')
Creating vector time with 32089 elements.
Creating vector conductivity with 32089 elements.
Creating vector time with 32089 elements.
Creating vector temperature with 32089 elements.
Creating vector time with 32089 elements.
Creating vector cond_frequency with 32089 elements.
Creating vector time with 32089 elements.
Creating vector temp_frequency with 32089 elements.
Creating vector time with 32089 elements.
Creating vector flow2 with 32089 elements.
Creating vector time with 32089 elements.
Creating vector spare with 32089 elements.
Creating vector time with 32089 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/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/2004/2004317/2004.317.02/isuslog.nc')
Creating vector time with 5163 elements.
Creating vector isusNitrate with 5163 elements.
Creating vector time with 5163 elements.
Creating vector isusTemp with 5163 elements.
Creating vector time with 5163 elements.
Creating vector isusQuality with 5163 elements.
Creating vector time with 5163 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/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/2004/2004317/2004.317.02/biolume.nc')
Creating vector time with 8057 elements.
Creating vector rrr with 8057 elements.
Creating vector time with 8057 elements.
Creating vector cal_striing with 8057 elements.
Creating vector time with 8057 elements.
Creating vector pump with 8057 elements.
Creating vector time with 8057 elements.
Creating vector flow with 8057 elements.
Creating vector time with 8057 elements.
Creating vector humidity with 8057 elements.
Creating vector time with 8057 elements.
Creating vector temperature with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_0 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_1 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_2 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_3 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_4 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_5 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_6 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_7 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_8 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_9 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_10 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_11 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_12 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_13 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_14 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_15 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_16 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_17 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_18 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_19 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_20 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_21 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_22 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_23 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_24 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_25 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_26 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_27 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_28 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_29 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_30 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_31 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_32 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_33 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_34 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_35 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_36 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_37 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_38 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_39 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_40 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_41 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_42 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_43 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_44 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_45 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_46 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_47 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_48 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_49 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_50 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_51 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_52 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_53 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_54 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_55 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_56 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_57 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_58 with 8057 elements.
Creating vector time with 8057 elements.
Creating vector raw_59 with 8057 elements.
Creating vector time with 8057 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004317/2004.317.02/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/2004/2004317/2004.317.02/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/2004/2004317/2004.317.02/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/2004/2004317/2004.317.02/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/2004/2004317/2004.317.02/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_2004.317.02.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_2004.317.00.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.317.01.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.317.02.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 13 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_317_00_317_02_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_317_00_317_02.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_317_00_317_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 = 128 Gridding with nix = 384, iZ = 199
Using mean boxcar filter of vector...
Using mean boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Gridding...
   T
   S
   O
Using median boxcar filter of vector...
Using median boxcar filter of vector...
Using median boxcar filter of vector...
   bbp470
[Warning: Duplicate data points have been detected and removed - corresponding
values have been averaged.] 
[> In griddata>useScatteredInterp (line 185)
  In griddata (line 126)
  In plot_sections (line 231)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
   bbp676
[Warning: Duplicate data points have been detected and removed - corresponding
values have been averaged.] 
[> In griddata>useScatteredInterp (line 185)
  In griddata (line 126)
  In plot_sections (line 253)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
   fl676_uncorr
[Warning: Duplicate data points have been detected and removed - corresponding
values have been averaged.] 
[> In griddata>useScatteredInterp (line 185)
  In griddata (line 126)
  In plot_sections (line 274)
  In create_data_products (line 119)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
   N
   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 139835 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 139835 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: 11/11/2004 17:30  to 11/12/2004 04:30 

swr =

    2.2347
    1.4108
    1.6446
    1.2753
    1.2253
    1.4489
    0.9414
    0.7876
    0.9210
    0.9667
    0.9624
    0.9548

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_317_00_317_02_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2004317_GulperTimes.txt && touch ../results/2004317_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/2004/2004317/2004.317.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004317/2004.317.00/syslog -startEsecs 1100253549.968 -surveyName Dorado389_2004_317_00_317_02 >> ../results/2004317_GulperTimes.txt
Executing: removeGulpDups.py ../results/2004317_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/2004/2004317/2004.317.01/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004317/2004.317.01/syslog -startEsecs 1100253549.968 -surveyName Dorado389_2004_317_00_317_02 >> ../results/2004317_GulperTimes.txt
Executing: removeGulpDups.py ../results/2004317_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/2004/2004317/2004.317.02/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004317/2004.317.02/syslog -startEsecs 1100253549.968 -surveyName Dorado389_2004_317_00_317_02 >> ../results/2004317_GulperTimes.txt
Executing: removeGulpDups.py ../results/2004317_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_317_00_317_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_317_00_317_02_2column.png
Elapsed time to save image: 9 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_317_00_317_02_biolume.png
Elapsed time to save image: 33 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_317_00_317_02_lopc.png
Elapsed time to save image: 9 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_317_00_317_02_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_317_00_317_02_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_317_00_317_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_317_00_317_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_317_00_317_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_317_00_317_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_317_00_317_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_317_00_317_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_317_00_317_02_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_317_00_317_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_317_00_317_02_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_317_00_317_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_317_00_317_02_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_317_00_317_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_317_00_317_02_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_317_00_317_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);
Could not do interp1: The grid vectors must contain unique points.
Did not write KML for this variable.  Rethrowing error.
Could not create .kmz for Optical Backscatter @470 nm
KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath);
Could not do interp1: The grid vectors must contain unique points.
Did not write KML for this variable.  Rethrowing error.
Could not create .kmz for Optical Backscatter @676 nm
KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath);
Could not do interp1: The grid vectors must contain unique points.
Did not write KML for this variable.  Rethrowing error.
Could not create .kmz for Chlorophyll Fluorescence   
KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath);
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_317_00_317_02_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_317_00_317_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_317_00_317_02.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_317_00_317_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_317_00_317_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_317_00_317_02.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
Encountered 840 NaN values in array of lon that is 18841 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 18001 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 18001 are not equal to number of Lat lon points = 18841
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_317_00_317_02.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_317_00_317_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_317_00_317_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_317_00_317_02_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_317_00_317_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_317_00_317_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_317_00_317_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_317_00_317_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_317_00_317_02 processed" mccann@mbari.org < mail_Dorado389_2004_317_00_317_02.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.317.00.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.317.01.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.317.02.mat
Processing time: 101 seconds