Execution of AUVprocess_main version 1.85 at 2014-03-18T09:25:22Z on elvis
Matlab command executed: 
   AUVprocess_main('LOCO', 2007, ['009.06'], '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: 2007.009.06
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/
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/2007/2007009/2007.009.06/navigation.nc')
Creating vector time with 40987 elements.
Creating vector mPos_x with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mPos_y with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mDepth with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mGpsNorth with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mGpsEast with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mGpsValid with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mPhi with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mTheta with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mPsi with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mOmega_x with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mOmega_y with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mOmega_z with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mPsaRange with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mAltitude with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mDvlAltitude with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mWaterSpeed with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mDvlValid with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mDvlNewData with 40987 elements.
Creating vector time with 40987 elements.
Creating vector mDeltaT with 40987 elements.
Creating vector time with 40987 elements.
Creating vector nfix with 40987 elements.
Creating vector time with 40987 elements.
Creating vector efix with 40987 elements.
Creating vector time with 40987 elements.
Creating vector filter_north with 40987 elements.
Creating vector time with 40987 elements.
Creating vector filter_east with 40987 elements.
Creating vector time with 40987 elements.
Creating vector filter_depth with 40987 elements.
Creating vector time with 40987 elements.
Creating vector north_current with 40987 elements.
Creating vector time with 40987 elements.
Creating vector east_current with 40987 elements.
Creating vector time with 40987 elements.
Creating vector speed_bias with 40987 elements.
Creating vector time with 40987 elements.
Creating vector heading_bias with 40987 elements.
Creating vector time with 40987 elements.
Creating vector latitude with 40987 elements.
Creating vector time with 40987 elements.
Creating vector longitude with 40987 elements.
Creating vector time with 40987 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/navigation.nc');
processNav(): median of positive valued depths = 3.799
processNav(): Finding depths less than 18.9949 and times > 0
processNav(): length(Nav.depth) = 40987
processNav(): length(gindx)     = 40987
 
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/2007/2007009/2007.009.06/gps.nc')
Creating vector time with 385 elements.
Creating vector hours with 385 elements.
Creating vector time with 385 elements.
Creating vector minutes with 385 elements.
Creating vector time with 385 elements.
Creating vector seconds with 385 elements.
Creating vector time with 385 elements.
Creating vector centiSeconds with 385 elements.
Creating vector time with 385 elements.
Creating vector latitude with 385 elements.
Creating vector time with 385 elements.
Creating vector longitude with 385 elements.
Creating vector time with 385 elements.
Creating vector quality with 385 elements.
Creating vector time with 385 elements.
Creating vector numberOfSatellites with 385 elements.
Creating vector time with 385 elements.
Creating vector hdop with 385 elements.
Creating vector time with 385 elements.
Creating vector antennaHeight with 385 elements.
Creating vector time with 385 elements.
Creating vector geoHeight with 385 elements.
Creating vector time with 385 elements.
Creating vector dgpsDataAge with 385 elements.
Creating vector time with 385 elements.
Creating vector dgpsRSID with 385 elements.
Creating vector time with 385 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/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/2007/2007009/2007.009.06/parosci.nc')
Creating vector time with 88150 elements.
Creating vector depth with 88150 elements.
Creating vector time with 88150 elements.
Creating vector temp with 88150 elements.
Creating vector time with 88150 elements.
Creating vector pressure with 88150 elements.
Creating vector time with 88150 elements.
Creating vector temp_period with 88150 elements.
Creating vector time with 88150 elements.
Creating vector pres_period with 88150 elements.
Creating vector time with 88150 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.27907 max(Depth.data) = 9.8199
Found 3326 bad (> 300 | < 0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = 0.00027154 max(Depth.data) = 9.8199
 
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/2007/2007009/2007.009.06/hydroscatlog.nc')
Creating vector time with 32930 elements.
Creating vector Seconds with 32930 elements.
Creating vector time with 32930 elements.
Creating vector HundrethsOfSeconds with 32930 elements.
Creating vector time with 32930 elements.
Creating vector Snorm1 with 32930 elements.
Creating vector time with 32930 elements.
Creating vector Snorm2 with 32930 elements.
Creating vector time with 32930 elements.
Creating vector Snorm3 with 32930 elements.
Creating vector time with 32930 elements.
Creating vector Gain_Status_1 with 32930 elements.
Creating vector time with 32930 elements.
Creating vector Gain_Status_2 with 32930 elements.
Creating vector time with 32930 elements.
Creating vector Gain_Status_3 with 32930 elements.
Creating vector time with 32930 elements.
Creating vector RawDepthValue with 32930 elements.
Creating vector time with 32930 elements.
Creating vector RawTempValue with 32930 elements.
Creating vector time with 32930 elements.
Creating vector Temperature with 32930 elements.
Creating vector time with 32930 elements.
Creating vector ErrorValue with 32930 elements.
Creating vector time with 32930 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/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/2007/2007009/2007.009.06/ctdDriver.nc')
Creating vector time with 32838 elements.
Creating vector conductivity with 32838 elements.
Creating vector time with 32838 elements.
Creating vector temperature with 32838 elements.
Creating vector time with 32838 elements.
Creating vector cond_frequency with 32838 elements.
Creating vector time with 32838 elements.
Creating vector temp_frequency with 32838 elements.
Creating vector time with 32838 elements.
Creating vector spare with 32838 elements.
Creating vector time with 32838 elements.
Creating vector humidity with 32838 elements.
Creating vector time with 32838 elements.
Creating vector flow1 with 32838 elements.
Creating vector time with 32838 elements.
Creating vector OBS with 32838 elements.
Creating vector time with 32838 elements.
Creating vector dissolvedO2 with 32838 elements.
Creating vector time with 32838 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/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/2007/2007009/2007.009.06/ctdDriver2.nc')
Creating vector time with 32841 elements.
Creating vector conductivity with 32841 elements.
Creating vector time with 32841 elements.
Creating vector temperature with 32841 elements.
Creating vector time with 32841 elements.
Creating vector cond_frequency with 32841 elements.
Creating vector time with 32841 elements.
Creating vector temp_frequency with 32841 elements.
Creating vector time with 32841 elements.
Creating vector flow2 with 32841 elements.
Creating vector time with 32841 elements.
Creating vector spare with 32841 elements.
Creating vector time with 32841 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/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/2007/2007009/2007.009.06/isuslog.nc')
Creating vector time with 5758 elements.
Creating vector isusNitrate with 5758 elements.
Creating vector time with 5758 elements.
Creating vector isusTemp with 5758 elements.
Creating vector time with 5758 elements.
Creating vector isusQuality with 5758 elements.
Creating vector time with 5758 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/isuslog.nc');
Total lag applied to nitrate = 6 seconds
 
Processing Biolume data...
{Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.} 
{> In rmpath at 58
  In processBiolume at 21
  In processAUVmission at 220
  In AUVprocess_main at 220
  In reprocess_surveys at 639} 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/biolume.nc')
Creating vector time with 8256 elements.
Creating vector rrr with 8256 elements.
Creating vector time with 8256 elements.
Creating vector cal_striing with 8256 elements.
Creating vector time with 8256 elements.
Creating vector pump with 8256 elements.
Creating vector time with 8256 elements.
Creating vector flow with 8256 elements.
Creating vector time with 8256 elements.
Creating vector humidity with 8256 elements.
Creating vector time with 8256 elements.
Creating vector temperature with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_0 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_1 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_2 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_3 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_4 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_5 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_6 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_7 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_8 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_9 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_10 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_11 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_12 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_13 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_14 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_15 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_16 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_17 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_18 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_19 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_20 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_21 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_22 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_23 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_24 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_25 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_26 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_27 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_28 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_29 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_30 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_31 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_32 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_33 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_34 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_35 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_36 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_37 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_38 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_39 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_40 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_41 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_42 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_43 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_44 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_45 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_46 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_47 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_48 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_49 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_50 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_51 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_52 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_53 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_54 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_55 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_56 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_57 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_58 with 8256 elements.
Creating vector time with 8256 elements.
Creating vector raw_59 with 8256 elements.
Creating vector time with 8256 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007009/2007.009.06/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/2007/2007009/2007.009.06/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/2007/2007009/2007.009.06/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/2007/2007009/2007.009.06/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/2007/2007009/2007.009.06/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_2007.009.06.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
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Calling build_auv_survey.m to construct survey file...

SecondaryDissolvedO2 =

     []

Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007.009.06.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 5 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_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 = 242 Gridding with nix = 726, iZ = 17
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 40756 elements long
! grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath
GMT_grd_is_global: no!
GMT_grd_is_global: no!
GMT_boundcond_param_prep determined edgeinfo: gn = 0, gs = 0, nxp = 0, nyp = 0
grdtrack: Sampled 40756 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 77897 elements.

urlSwrData =

http://elvis.shore.mbari.org/thredds/dodsC/agg/OS_MBARI-M1_R_M?SW[19424:1:19428][0:1:0][0:1:0][0:1:0]

Creating matrix SW (5 x 1 x 1 x 1) with 5 elements.
Creating vector TIME with 5 elements.
Creating vector DEPTH with 1 elements.
Creating vector LATITUDE with 1 elements.
Creating vector LONGITUDE with 1 elements.
SWR data read from OPeNDAP has time range: 01/09/2007 11:30  to 01/09/2007 15:29 

swr =

  491.8680
  521.3087
  478.6806
  383.3475
  247.7017

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2007009_GulperTimes.txt && touch ../results/2007009_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/2007/2007009/2007.009.06/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2007/2007009/2007.009.06/syslog -startEsecs 1168374933.5226 -surveyName Dorado389_2007_009_06_009_06 >> ../results/2007009_GulperTimes.txt
Executing: perl removeGulpDups.pl ../results/2007009_GulperTimes.txt
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_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 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_2007_009_06_009_06_2column.png
Elapsed time to save image: 3 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_2007_009_06_009_06_biolume.png
Elapsed time to save image: 18 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_2007_009_06_009_06_lopc.png
Elapsed time to save image: 3 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_2007_009_06_009_06_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_2column.png...
Copied to /mbari/AUVCTD/surveys/2007/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_biolume.png...
Copied to /mbari/AUVCTD/surveys/2007/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_lopc.png...
Copied to /mbari/AUVCTD/surveys/2007/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2007/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2007/images/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2007/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_2007_009_06_009_06_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_009_06_009_06_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2007/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_2007_009_06_009_06_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_009_06_009_06_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2007/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_2007_009_06_009_06_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_009_06_009_06_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2007/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_2007_009_06_009_06_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_009_06_009_06_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2007/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_2007_009_06_009_06_Optical_Backscatter_470_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_009_06_009_06_Optical_Backscatter_470_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2007/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_2007_009_06_009_06_Optical_Backscatter_676_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_009_06_009_06_Optical_Backscatter_676_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2007/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_2007_009_06_009_06_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_009_06_009_06_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2007/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_2007_009_06_009_06_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_009_06_009_06_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2007/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_2007_009_06_009_06_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_009_06_009_06_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2007/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Creating Dorado389_2007_009_06_009_06.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06.kml...
Copied to /mbari/AUVCTD/surveys/2007/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
{Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_009_06_009_06_LOPC_Total_Count.kml' not found.} 
{> In create_data_products at 412
  In build_auv_survey at 497
  In AUVprocess_main at 250
  In reprocess_surveys at 639} 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpRed.  Interpolating anyway.
Encountered 34 NaN values in array of lon that is 5756 elements long
! grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath
GMT_grd_is_global: no!
GMT_grd_is_global: no!
GMT_boundcond_param_prep determined edgeinfo: gn = 0, gs = 0, nxp = 0, nyp = 0
grdtrack: Sampled 5722 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 5722 are not equal to number of Lat lon points = 5756
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_2007_009_06_009_06.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06.txt...
Copied to /mbari/AUVCTD/surveys/2007/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_Gulper.txt...
Tried, but failed to copy to /mbari/AUVCTD/surveys/2007/odv/
cp: cannot stat `/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_Gulper.txt': No such file or directory

 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpRed.  Interpolating anyway.
Saving Global Attributes
Saving Variables and attributes
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_decim.nc...
Copied to /mbari/AUVCTD/surveys/2007/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_2007_009_06_009_06.nc...
Copied to /mbari/AUVCTD/surveys/2007/netcdf/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2007/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_009_06_009_06.mat...
Copied to /mbari/AUVCTD/surveys/2007/mat/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2007_009_06_009_06 processed" mccann@mbari.org < mail_Dorado389_2007_009_06_009_06.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007.009.06.mat
Processing time: 90 seconds