Execution of AUVprocess_main version 1.86 at 2018-05-31T18:07:57Z on elvis
Matlab command executed: 
   AUVprocess_main('BIOLUME', 2004, ['096.03';'096.05';'096.06'], '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: 2004.096.03
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/
Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Processing DVL navigation data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/navigation.nc')
Creating vector time with 13124 elements.
Creating vector mPos_x with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mPos_y with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mDepth with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mGpsNorth with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mGpsEast with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mGpsValid with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mPhi with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mTheta with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mPsi with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mOmega_x with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mOmega_y with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mOmega_z with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mPsaRange with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mAltitude with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mWaterSpeed with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mDvlValid with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mDvlNewData with 13124 elements.
Creating vector time with 13124 elements.
Creating vector mDeltaT with 13124 elements.
Creating vector time with 13124 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/navigation.nc');
processNav(): median of positive valued depths = 50.4934
processNav(): Finding depths less than 353.4535 and times > 0
processNav(): length(Nav.depth) = 13124
processNav(): length(gindx)     = 13124
 
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/2004/2004096/2004.096.03/gps.nc')
Creating vector time with 435 elements.
Creating vector hours with 435 elements.
Creating vector time with 435 elements.
Creating vector minutes with 435 elements.
Creating vector time with 435 elements.
Creating vector seconds with 435 elements.
Creating vector time with 435 elements.
Creating vector centiSeconds with 435 elements.
Creating vector time with 435 elements.
Creating vector latitude with 435 elements.
Creating vector time with 435 elements.
Creating vector longitude with 435 elements.
Creating vector time with 435 elements.
Creating vector quality with 435 elements.
Creating vector time with 435 elements.
Creating vector numberOfSatellites with 435 elements.
Creating vector time with 435 elements.
Creating vector hdop with 435 elements.
Creating vector time with 435 elements.
Creating vector antennaHeight with 435 elements.
Creating vector time with 435 elements.
Creating vector geoHeight with 435 elements.
Creating vector time with 435 elements.
Creating vector dgpsDataAge with 435 elements.
Creating vector time with 435 elements.
Creating vector dgpsRSID with 435 elements.
Creating vector time with 435 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/gps.nc');
 
Processing depth data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/parosci.nc')
Creating vector time with 13231 elements.
Creating vector depth with 13231 elements.
Creating vector time with 13231 elements.
Creating vector temp with 13231 elements.
Creating vector time with 13231 elements.
Creating vector pressure with 13231 elements.
Creating vector time with 13231 elements.
Creating vector temp_period with 13231 elements.
Creating vector time with 13231 elements.
Creating vector pres_period with 13231 elements.
Creating vector time with 13231 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.27198 max(Depth.data) = 100.6539
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.27198 max(Depth.data) = 100.6539
 
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/2004/2004096/2004.096.03/hydroscatlog.nc')
Creating vector time with 10565 elements.
Creating vector Seconds with 10565 elements.
Creating vector time with 10565 elements.
Creating vector HundrethsOfSeconds with 10565 elements.
Creating vector time with 10565 elements.
Creating vector Snorm1 with 10565 elements.
Creating vector time with 10565 elements.
Creating vector Snorm2 with 10565 elements.
Creating vector time with 10565 elements.
Creating vector Snorm3 with 10565 elements.
Creating vector time with 10565 elements.
Creating vector Gain_Status_1 with 10565 elements.
Creating vector time with 10565 elements.
Creating vector Gain_Status_2 with 10565 elements.
Creating vector time with 10565 elements.
Creating vector Gain_Status_3 with 10565 elements.
Creating vector time with 10565 elements.
Creating vector RawDepthValue with 10565 elements.
Creating vector time with 10565 elements.
Creating vector RawTempValue with 10565 elements.
Creating vector time with 10565 elements.
Creating vector Temperature with 10565 elements.
Creating vector time with 10565 elements.
Creating vector ErrorValue with 10565 elements.
Creating vector time with 10565 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/hydroscatlog.nc');
 
Processing CTD #1 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/ctdDriver.nc')
Creating vector time with 10509 elements.
Creating vector conductivity with 10509 elements.
Creating vector time with 10509 elements.
Creating vector temperature with 10509 elements.
Creating vector time with 10509 elements.
Creating vector cond_frequency with 10509 elements.
Creating vector time with 10509 elements.
Creating vector temp_frequency with 10509 elements.
Creating vector time with 10509 elements.
Creating vector spare with 10509 elements.
Creating vector time with 10509 elements.
Creating vector humidity with 10509 elements.
Creating vector time with 10509 elements.
Creating vector flow1 with 10509 elements.
Creating vector time with 10509 elements.
Creating vector OBS with 10509 elements.
Creating vector time with 10509 elements.
Creating vector dissolvedO2 with 10509 elements.
Creating vector time with 10509 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/ctdDriver.cfg
Oxygen calibration loaded from CTD config file (current method)
Using constant flow rate offset for oxygen...
 
Processing CTD #2 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/ctdDriver2.nc')
Creating vector time with 10508 elements.
Creating vector conductivity with 10508 elements.
Creating vector time with 10508 elements.
Creating vector temperature with 10508 elements.
Creating vector time with 10508 elements.
Creating vector cond_frequency with 10508 elements.
Creating vector time with 10508 elements.
Creating vector temp_frequency with 10508 elements.
Creating vector time with 10508 elements.
Creating vector flow2 with 10508 elements.
Creating vector time with 10508 elements.
Creating vector spare with 10508 elements.
Creating vector time with 10508 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/ctdDriver2.cfg
 
Processing ISUS data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/isuslog.nc')
Creating vector time with 1563 elements.
Creating vector isusNitrate with 1563 elements.
Creating vector time with 1563 elements.
Creating vector isusTemp with 1563 elements.
Creating vector time with 1563 elements.
Creating vector isusQuality with 1563 elements.
Creating vector time with 1563 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/isuslog.nc');
Total lag applied to nitrate = 6 seconds
 
Processing Biolume data...
[Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 75)
  In processBiolume (line 21)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
[Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 75)
  In processBiolume (line 22)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/biolume.nc')
Creating vector time with 2648 elements.
Creating vector rrr with 2648 elements.
Creating vector time with 2648 elements.
Creating vector cal_striing with 2648 elements.
Creating vector time with 2648 elements.
Creating vector pump with 2648 elements.
Creating vector time with 2648 elements.
Creating vector flow with 2648 elements.
Creating vector time with 2648 elements.
Creating vector humidity with 2648 elements.
Creating vector time with 2648 elements.
Creating vector temperature with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_0 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_1 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_2 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_3 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_4 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_5 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_6 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_7 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_8 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_9 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_10 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_11 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_12 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_13 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_14 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_15 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_16 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_17 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_18 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_19 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_20 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_21 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_22 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_23 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_24 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_25 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_26 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_27 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_28 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_29 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_30 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_31 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_32 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_33 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_34 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_35 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_36 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_37 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_38 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_39 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_40 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_41 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_42 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_43 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_44 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_45 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_46 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_47 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_48 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_49 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_50 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_51 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_52 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_53 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_54 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_55 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_56 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_57 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_58 with 2648 elements.
Creating vector time with 2648 elements.
Creating vector raw_59 with 2648 elements.
Creating vector time with 2648 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/lopc.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/lopc.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/lopc.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.03/lopc.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


*** Setting lopc structure to NaNs. *** 
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.096.03.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
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Processing AUV mission: 2004.096.05
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/
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/2004/2004096/2004.096.05/navigation.nc')
Creating vector time with 11915 elements.
Creating vector mPos_x with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mPos_y with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mDepth with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mGpsNorth with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mGpsEast with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mGpsValid with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mPhi with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mTheta with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mPsi with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mOmega_x with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mOmega_y with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mOmega_z with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mPsaRange with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mAltitude with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mWaterSpeed with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mDvlValid with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mDvlNewData with 11915 elements.
Creating vector time with 11915 elements.
Creating vector mDeltaT with 11915 elements.
Creating vector time with 11915 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/navigation.nc');
processNav(): median of positive valued depths = 50.6405
processNav(): Finding depths less than 354.4832 and times > 0
processNav(): length(Nav.depth) = 11915
processNav(): length(gindx)     = 11915
 
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/2004/2004096/2004.096.05/gps.nc')
Creating vector time with 205 elements.
Creating vector hours with 205 elements.
Creating vector time with 205 elements.
Creating vector minutes with 205 elements.
Creating vector time with 205 elements.
Creating vector seconds with 205 elements.
Creating vector time with 205 elements.
Creating vector centiSeconds with 205 elements.
Creating vector time with 205 elements.
Creating vector latitude with 205 elements.
Creating vector time with 205 elements.
Creating vector longitude with 205 elements.
Creating vector time with 205 elements.
Creating vector quality with 205 elements.
Creating vector time with 205 elements.
Creating vector numberOfSatellites with 205 elements.
Creating vector time with 205 elements.
Creating vector hdop with 205 elements.
Creating vector time with 205 elements.
Creating vector antennaHeight with 205 elements.
Creating vector time with 205 elements.
Creating vector geoHeight with 205 elements.
Creating vector time with 205 elements.
Creating vector dgpsDataAge with 205 elements.
Creating vector time with 205 elements.
Creating vector dgpsRSID with 205 elements.
Creating vector time with 205 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/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/2004/2004096/2004.096.05/parosci.nc')
Creating vector time with 12020 elements.
Creating vector depth with 12020 elements.
Creating vector time with 12020 elements.
Creating vector temp with 12020 elements.
Creating vector time with 12020 elements.
Creating vector pressure with 12020 elements.
Creating vector time with 12020 elements.
Creating vector temp_period with 12020 elements.
Creating vector time with 12020 elements.
Creating vector pres_period with 12020 elements.
Creating vector time with 12020 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.58404 max(Depth.data) = 100.6946
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.58404 max(Depth.data) = 100.6946
 
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/2004/2004096/2004.096.05/hydroscatlog.nc')
Creating vector time with 9601 elements.
Creating vector Seconds with 9601 elements.
Creating vector time with 9601 elements.
Creating vector HundrethsOfSeconds with 9601 elements.
Creating vector time with 9601 elements.
Creating vector Snorm1 with 9601 elements.
Creating vector time with 9601 elements.
Creating vector Snorm2 with 9601 elements.
Creating vector time with 9601 elements.
Creating vector Snorm3 with 9601 elements.
Creating vector time with 9601 elements.
Creating vector Gain_Status_1 with 9601 elements.
Creating vector time with 9601 elements.
Creating vector Gain_Status_2 with 9601 elements.
Creating vector time with 9601 elements.
Creating vector Gain_Status_3 with 9601 elements.
Creating vector time with 9601 elements.
Creating vector RawDepthValue with 9601 elements.
Creating vector time with 9601 elements.
Creating vector RawTempValue with 9601 elements.
Creating vector time with 9601 elements.
Creating vector Temperature with 9601 elements.
Creating vector time with 9601 elements.
Creating vector ErrorValue with 9601 elements.
Creating vector time with 9601 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/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/2004/2004096/2004.096.05/ctdDriver.nc')
Creating vector time with 9576 elements.
Creating vector conductivity with 9576 elements.
Creating vector time with 9576 elements.
Creating vector temperature with 9576 elements.
Creating vector time with 9576 elements.
Creating vector cond_frequency with 9576 elements.
Creating vector time with 9576 elements.
Creating vector temp_frequency with 9576 elements.
Creating vector time with 9576 elements.
Creating vector spare with 9576 elements.
Creating vector time with 9576 elements.
Creating vector humidity with 9576 elements.
Creating vector time with 9576 elements.
Creating vector flow1 with 9576 elements.
Creating vector time with 9576 elements.
Creating vector OBS with 9576 elements.
Creating vector time with 9576 elements.
Creating vector dissolvedO2 with 9576 elements.
Creating vector time with 9576 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/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/2004/2004096/2004.096.05/ctdDriver2.nc')
Creating vector time with 9575 elements.
Creating vector conductivity with 9575 elements.
Creating vector time with 9575 elements.
Creating vector temperature with 9575 elements.
Creating vector time with 9575 elements.
Creating vector cond_frequency with 9575 elements.
Creating vector time with 9575 elements.
Creating vector temp_frequency with 9575 elements.
Creating vector time with 9575 elements.
Creating vector flow2 with 9575 elements.
Creating vector time with 9575 elements.
Creating vector spare with 9575 elements.
Creating vector time with 9575 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/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/2004/2004096/2004.096.05/isuslog.nc')
Creating vector time with 1415 elements.
Creating vector isusNitrate with 1415 elements.
Creating vector time with 1415 elements.
Creating vector isusTemp with 1415 elements.
Creating vector time with 1415 elements.
Creating vector isusQuality with 1415 elements.
Creating vector time with 1415 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/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/2004/2004096/2004.096.05/biolume.nc')
Creating vector time with 2406 elements.
Creating vector rrr with 2406 elements.
Creating vector time with 2406 elements.
Creating vector cal_striing with 2406 elements.
Creating vector time with 2406 elements.
Creating vector pump with 2406 elements.
Creating vector time with 2406 elements.
Creating vector flow with 2406 elements.
Creating vector time with 2406 elements.
Creating vector humidity with 2406 elements.
Creating vector time with 2406 elements.
Creating vector temperature with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_0 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_1 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_2 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_3 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_4 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_5 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_6 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_7 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_8 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_9 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_10 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_11 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_12 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_13 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_14 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_15 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_16 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_17 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_18 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_19 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_20 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_21 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_22 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_23 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_24 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_25 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_26 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_27 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_28 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_29 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_30 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_31 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_32 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_33 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_34 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_35 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_36 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_37 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_38 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_39 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_40 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_41 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_42 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_43 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_44 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_45 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_46 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_47 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_48 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_49 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_50 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_51 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_52 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_53 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_54 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_55 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_56 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_57 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_58 with 2406 elements.
Creating vector time with 2406 elements.
Creating vector raw_59 with 2406 elements.
Creating vector time with 2406 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.05/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/2004/2004096/2004.096.05/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/2004/2004096/2004.096.05/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/2004/2004096/2004.096.05/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/2004/2004096/2004.096.05/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_2004.096.05.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2004.096.06
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/
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/2004/2004096/2004.096.06/navigation.nc')
Creating vector time with 59252 elements.
Creating vector mPos_x with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mPos_y with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mDepth with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mGpsNorth with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mGpsEast with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mGpsValid with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mPhi with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mTheta with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mPsi with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mOmega_x with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mOmega_y with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mOmega_z with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mPsaRange with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mAltitude with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mWaterSpeed with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mDvlValid with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mDvlNewData with 59252 elements.
Creating vector time with 59252 elements.
Creating vector mDeltaT with 59252 elements.
Creating vector time with 59252 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/navigation.nc');
processNav(): median of positive valued depths = 51.4752
processNav(): Finding depths less than 360.3266 and times > 0
processNav(): length(Nav.depth) = 59252
processNav(): length(gindx)     = 59252
 
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/2004/2004096/2004.096.06/gps.nc')
Creating vector time with 412 elements.
Creating vector hours with 412 elements.
Creating vector time with 412 elements.
Creating vector minutes with 412 elements.
Creating vector time with 412 elements.
Creating vector seconds with 412 elements.
Creating vector time with 412 elements.
Creating vector centiSeconds with 412 elements.
Creating vector time with 412 elements.
Creating vector latitude with 412 elements.
Creating vector time with 412 elements.
Creating vector longitude with 412 elements.
Creating vector time with 412 elements.
Creating vector quality with 412 elements.
Creating vector time with 412 elements.
Creating vector numberOfSatellites with 412 elements.
Creating vector time with 412 elements.
Creating vector hdop with 412 elements.
Creating vector time with 412 elements.
Creating vector antennaHeight with 412 elements.
Creating vector time with 412 elements.
Creating vector geoHeight with 412 elements.
Creating vector time with 412 elements.
Creating vector dgpsDataAge with 412 elements.
Creating vector time with 412 elements.
Creating vector dgpsRSID with 412 elements.
Creating vector time with 412 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/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/2004/2004096/2004.096.06/parosci.nc')
Creating vector time with 59358 elements.
Creating vector depth with 59358 elements.
Creating vector time with 59358 elements.
Creating vector temp with 59358 elements.
Creating vector time with 59358 elements.
Creating vector pressure with 59358 elements.
Creating vector time with 59358 elements.
Creating vector temp_period with 59358 elements.
Creating vector time with 59358 elements.
Creating vector pres_period with 59358 elements.
Creating vector time with 59358 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.12832 max(Depth.data) = 100.9247
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.12832 max(Depth.data) = 100.9247
 
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/2004/2004096/2004.096.06/hydroscatlog.nc')
Creating vector time with 47452 elements.
Creating vector Seconds with 47452 elements.
Creating vector time with 47452 elements.
Creating vector HundrethsOfSeconds with 47452 elements.
Creating vector time with 47452 elements.
Creating vector Snorm1 with 47452 elements.
Creating vector time with 47452 elements.
Creating vector Snorm2 with 47452 elements.
Creating vector time with 47452 elements.
Creating vector Snorm3 with 47452 elements.
Creating vector time with 47452 elements.
Creating vector Gain_Status_1 with 47452 elements.
Creating vector time with 47452 elements.
Creating vector Gain_Status_2 with 47452 elements.
Creating vector time with 47452 elements.
Creating vector Gain_Status_3 with 47452 elements.
Creating vector time with 47452 elements.
Creating vector RawDepthValue with 47452 elements.
Creating vector time with 47452 elements.
Creating vector RawTempValue with 47452 elements.
Creating vector time with 47452 elements.
Creating vector Temperature with 47452 elements.
Creating vector time with 47452 elements.
Creating vector ErrorValue with 47452 elements.
Creating vector time with 47452 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/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/2004/2004096/2004.096.06/ctdDriver.nc')
Creating vector time with 47412 elements.
Creating vector conductivity with 47412 elements.
Creating vector time with 47412 elements.
Creating vector temperature with 47412 elements.
Creating vector time with 47412 elements.
Creating vector cond_frequency with 47412 elements.
Creating vector time with 47412 elements.
Creating vector temp_frequency with 47412 elements.
Creating vector time with 47412 elements.
Creating vector spare with 47412 elements.
Creating vector time with 47412 elements.
Creating vector humidity with 47412 elements.
Creating vector time with 47412 elements.
Creating vector flow1 with 47412 elements.
Creating vector time with 47412 elements.
Creating vector OBS with 47412 elements.
Creating vector time with 47412 elements.
Creating vector dissolvedO2 with 47412 elements.
Creating vector time with 47412 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/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/2004/2004096/2004.096.06/ctdDriver2.nc')
Creating vector time with 47411 elements.
Creating vector conductivity with 47411 elements.
Creating vector time with 47411 elements.
Creating vector temperature with 47411 elements.
Creating vector time with 47411 elements.
Creating vector cond_frequency with 47411 elements.
Creating vector time with 47411 elements.
Creating vector temp_frequency with 47411 elements.
Creating vector time with 47411 elements.
Creating vector flow2 with 47411 elements.
Creating vector time with 47411 elements.
Creating vector spare with 47411 elements.
Creating vector time with 47411 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/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/2004/2004096/2004.096.06/isuslog.nc')
Creating vector time with 7164 elements.
Creating vector isusNitrate with 7164 elements.
Creating vector time with 7164 elements.
Creating vector isusTemp with 7164 elements.
Creating vector time with 7164 elements.
Creating vector isusQuality with 7164 elements.
Creating vector time with 7164 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/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/2004/2004096/2004.096.06/biolume.nc')
Creating vector time with 11874 elements.
Creating vector rrr with 11874 elements.
Creating vector time with 11874 elements.
Creating vector cal_striing with 11874 elements.
Creating vector time with 11874 elements.
Creating vector pump with 11874 elements.
Creating vector time with 11874 elements.
Creating vector flow with 11874 elements.
Creating vector time with 11874 elements.
Creating vector humidity with 11874 elements.
Creating vector time with 11874 elements.
Creating vector temperature with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_0 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_1 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_2 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_3 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_4 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_5 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_6 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_7 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_8 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_9 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_10 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_11 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_12 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_13 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_14 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_15 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_16 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_17 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_18 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_19 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_20 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_21 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_22 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_23 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_24 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_25 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_26 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_27 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_28 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_29 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_30 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_31 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_32 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_33 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_34 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_35 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_36 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_37 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_38 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_39 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_40 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_41 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_42 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_43 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_44 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_45 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_46 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_47 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_48 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_49 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_50 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_51 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_52 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_53 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_54 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_55 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_56 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_57 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_58 with 11874 elements.
Creating vector time with 11874 elements.
Creating vector raw_59 with 11874 elements.
Creating vector time with 11874 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004096/2004.096.06/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/2004/2004096/2004.096.06/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/2004/2004096/2004.096.06/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/2004/2004096/2004.096.06/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/2004/2004096/2004.096.06/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_2004.096.06.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_2004.096.03.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.096.05.mat
Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.096.06.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 7 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06.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 = 60 Gridding with nix = 180, iZ = 199
Using mean boxcar filter of vector...
Using mean boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Using max boxcar filter of vector...
Gridding...
   T
   S
   O
Using median boxcar filter of vector...
Using median boxcar filter of vector...
Using median boxcar filter of vector...
   bbp470
   bbp676
   fl676_uncorr
   N
   BL
   BLflow
   LOPC
Only one good point or fewer - NaNing the gLOPCcount array.
                             - NaNing the gLOPCtransCount array.
                             - NaNing the gLOPCnonTransCount array.
                             - NaNing the gLOPCLCcount array.
 
Masking and filtering with median filter of size 5...
  cvarname = gT
  cvarname = gS
  cvarname = gO
  cvarname = gN
  cvarname = gF
  cvarname = gB470
  cvarname = gB676
  cvarname = gBL
  cvarname = gBLflow
  cvarname = gLOPCcount
No valid data for gLOPCcount
  cvarname = gLOPCtransCount
No valid data for gLOPCtransCount
  cvarname = gLOPCnonTransCount
No valid data for gLOPCnonTransCount
  cvarname = gLOPCLCcount
No valid data for gLOPCLCcount
Encountered 0 NaN values in array of lon that is 84194 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 84194 points from grid Monterey25.grd (2876 x 2447)
Getting short wave radiation data from M1 for little plot above the biolume section plot
Creating vector TIME with 119063 elements.
*** Could not find start or end index in Met data read from http://elvis.shore.mbari.org/thredds/dodsC/agg/OS_MBARI-M1_R_M
Looking for start days = 19818.2067 since 1/1/1950
Looking for end   days = 19818.4141
sIndx = 
eIndx = 
Met data goes from 20017.6042 to 24987.6875
No SWR data loaded from URL.
Executing: /bin/rm -f ../results/2004096_GulperTimes.txt && touch ../results/2004096_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/2004/2004096/2004.096.03/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004096/2004.096.03/syslog -startEsecs 1081147128.6872 -surveyName Dorado389_2004_096_03_096_06 >> ../results/2004096_GulperTimes.txt
Executing: removeGulpDups.py ../results/2004096_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/2004/2004096/2004.096.05/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004096/2004.096.05/syslog -startEsecs 1081147128.6872 -surveyName Dorado389_2004_096_03_096_06 >> ../results/2004096_GulperTimes.txt
Executing: removeGulpDups.py ../results/2004096_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/2004/2004096/2004.096.06/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004096/2004.096.06/syslog -startEsecs 1081147128.6872 -surveyName Dorado389_2004_096_03_096_06 >> ../results/2004096_GulperTimes.txt
Executing: removeGulpDups.py ../results/2004096_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06_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
2Column contouring gridded variable gT
2Column contouring gridded variable gS
2Column contouring gridded variable gN
2Column contouring gridded variable gO
2Column contouring gridded variable gB470
2Column contouring gridded variable gB676
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Did not add swr plot to the image.
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06_2column.png
Elapsed time to save image: 5 seconds
Biolume contouring gridded variable gD
Biolume contouring gridded variable gT
Biolume contouring gridded variable gS
Biolume contouring gridded variable gN
Biolume contouring gridded variable gO
Biolume contouring gridded variable gB470
Biolume contouring gridded variable gB676
Biolume contouring gridded variable gF
Biolume contouring gridded variable gBL
SWR image not added to the plot.
Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06_biolume.png
Elapsed time to save image: 25 seconds
2Column contouring gridded variable gLOPCcount
2Column contouring gridded variable gLOPCtransCount
2Column contouring gridded variable gLOPCnonTransCount
2Column contouring gridded variable gLOPCLCcount
2Column contouring gridded variable gT
2Column contouring gridded variable gB470
2Column contouring gridded variable gB676
2Column contouring gridded variable gF
2Column contouring gridded variable gBL
Did not add swr plot to the image.
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06_lopc.png
Elapsed time to save image: 5 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_096_03_096_06_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06_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_096_03_096_06_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_096_03_096_06_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_096_03_096_06_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_096_03_096_06_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_096_03_096_06_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_096_03_096_06_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_096_03_096_06_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_096_03_096_06_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_096_03_096_06_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_096_03_096_06_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_096_03_096_06_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_096_03_096_06_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_096_03_096_06_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_096_03_096_06_Optical_Backscatter_470_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_096_03_096_06_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_096_03_096_06_Optical_Backscatter_676_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_096_03_096_06_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_096_03_096_06_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_096_03_096_06_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);
  adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_096_03_096_06_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_096_03_096_06_Bioluminescence.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, '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_096_03_096_06_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_096_03_096_06_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_096_03_096_06.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06.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_096_03_096_06_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_096_03_096_06.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
3 NaNs found in bbpBlue.  Interpolating anyway.
4 NaNs found in bbpRed.  Interpolating anyway.
3 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 13 NaN values in array of lon that is 10142 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 10129 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 10129 are not equal to number of Lat lon points = 10142
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_096_03_096_06.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06.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_096_03_096_06_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_096_03_096_06_Gulper.txt’: No such file or directory
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
3 NaNs found in bbpBlue.  Interpolating anyway.
4 NaNs found in bbpRed.  Interpolating anyway.
3 NaNs found in flRed_uncorr.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_096_03_096_06_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_096_03_096_06.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_096_03_096_06_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_096_03_096_06.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_096_03_096_06 processed" mccann@mbari.org < mail_Dorado389_2004_096_03_096_06.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.096.03.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.096.05.mat
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.096.06.mat
Processing time: 174 seconds