Execution of AUVprocess_main version 1.86 at 2018-05-30T05:30:21Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2007, ['211.02'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1')
 
*************************************************************************
Processing data from SSDS via DODS server
*************************************************************************
 
 
*************************************************************************
Processing AUV mission: 2007.211.02
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/
Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
Processing DVL navigation data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/navigation.nc')
Creating vector time with 366123 elements.
Creating vector mPos_x with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mPos_y with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mDepth with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mGpsNorth with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mGpsEast with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mGpsValid with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mPhi with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mTheta with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mPsi with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mOmega_x with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mOmega_y with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mOmega_z with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mPsaRange with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mAltitude with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mDvlAltitude with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mWaterSpeed with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mDvlValid with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mDvlNewData with 366123 elements.
Creating vector time with 366123 elements.
Creating vector mDeltaT with 366123 elements.
Creating vector time with 366123 elements.
Creating vector nfix with 366123 elements.
Creating vector time with 366123 elements.
Creating vector efix with 366123 elements.
Creating vector time with 366123 elements.
Creating vector filter_north with 366123 elements.
Creating vector time with 366123 elements.
Creating vector filter_east with 366123 elements.
Creating vector time with 366123 elements.
Creating vector filter_depth with 366123 elements.
Creating vector time with 366123 elements.
Creating vector north_current with 366123 elements.
Creating vector time with 366123 elements.
Creating vector east_current with 366123 elements.
Creating vector time with 366123 elements.
Creating vector speed_bias with 366123 elements.
Creating vector time with 366123 elements.
Creating vector heading_bias with 366123 elements.
Creating vector time with 366123 elements.
Creating vector latitude with 366123 elements.
Creating vector time with 366123 elements.
Creating vector longitude with 366123 elements.
Creating vector time with 366123 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/navigation.nc');
processNav(): median of positive valued depths = 90.5512
processNav(): Finding depths less than 633.8585 and times > 0
processNav(): length(Nav.depth) = 366123
processNav(): length(gindx)     = 366123
 
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/2007/2007211/2007.211.02/gps.nc')
Creating vector time with 2854 elements.
Creating vector hours with 2854 elements.
Creating vector time with 2854 elements.
Creating vector minutes with 2854 elements.
Creating vector time with 2854 elements.
Creating vector seconds with 2854 elements.
Creating vector time with 2854 elements.
Creating vector centiSeconds with 2854 elements.
Creating vector time with 2854 elements.
Creating vector latitude with 2854 elements.
Creating vector time with 2854 elements.
Creating vector longitude with 2854 elements.
Creating vector time with 2854 elements.
Creating vector quality with 2854 elements.
Creating vector time with 2854 elements.
Creating vector numberOfSatellites with 2854 elements.
Creating vector time with 2854 elements.
Creating vector hdop with 2854 elements.
Creating vector time with 2854 elements.
Creating vector antennaHeight with 2854 elements.
Creating vector time with 2854 elements.
Creating vector geoHeight with 2854 elements.
Creating vector time with 2854 elements.
Creating vector dgpsDataAge with 2854 elements.
Creating vector time with 2854 elements.
Creating vector dgpsRSID with 2854 elements.
Creating vector time with 2854 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/gps.nc');
 
Processing depth data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/parosci.nc')
Creating vector time with 642830 elements.
Creating vector depth with 642830 elements.
Creating vector time with 642830 elements.
Creating vector temp with 642830 elements.
Creating vector time with 642830 elements.
Creating vector pressure with 642830 elements.
Creating vector time with 642830 elements.
Creating vector temp_period with 642830 elements.
Creating vector time with 642830 elements.
Creating vector pres_period with 642830 elements.
Creating vector time with 642830 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.36209 max(Depth.data) = 250.7812
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.36209 max(Depth.data) = 250.7812
 
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/2007/2007211/2007.211.02/hydroscatlog.nc')
Creating vector time with 292925 elements.
Creating vector Seconds with 292925 elements.
Creating vector time with 292925 elements.
Creating vector HundrethsOfSeconds with 292925 elements.
Creating vector time with 292925 elements.
Creating vector Snorm1 with 292925 elements.
Creating vector time with 292925 elements.
Creating vector Snorm2 with 292925 elements.
Creating vector time with 292925 elements.
Creating vector Snorm3 with 292925 elements.
Creating vector time with 292925 elements.
Creating vector Gain_Status_1 with 292925 elements.
Creating vector time with 292925 elements.
Creating vector Gain_Status_2 with 292925 elements.
Creating vector time with 292925 elements.
Creating vector Gain_Status_3 with 292925 elements.
Creating vector time with 292925 elements.
Creating vector RawDepthValue with 292925 elements.
Creating vector time with 292925 elements.
Creating vector RawTempValue with 292925 elements.
Creating vector time with 292925 elements.
Creating vector Temperature with 292925 elements.
Creating vector time with 292925 elements.
Creating vector ErrorValue with 292925 elements.
Creating vector time with 292925 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/hydroscatlog.nc');
 
Processing CTD #1 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/ctdDriver.nc')
Creating vector time with 292945 elements.
Creating vector conductivity with 292945 elements.
Creating vector time with 292945 elements.
Creating vector temperature with 292945 elements.
Creating vector time with 292945 elements.
Creating vector cond_frequency with 292945 elements.
Creating vector time with 292945 elements.
Creating vector temp_frequency with 292945 elements.
Creating vector time with 292945 elements.
Creating vector spare with 292945 elements.
Creating vector time with 292945 elements.
Creating vector humidity with 292945 elements.
Creating vector time with 292945 elements.
Creating vector flow1 with 292945 elements.
Creating vector time with 292945 elements.
Creating vector OBS with 292945 elements.
Creating vector time with 292945 elements.
Creating vector dissolvedO2 with 292945 elements.
Creating vector time with 292945 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/ctdDriver.cfg
Oxygen calibration loaded from CTD config file (current method)
Using constant flow rate offset for oxygen...
 
Processing CTD #2 data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/ctdDriver2.nc')
Creating vector time with 292941 elements.
Creating vector conductivity with 292941 elements.
Creating vector time with 292941 elements.
Creating vector temperature with 292941 elements.
Creating vector time with 292941 elements.
Creating vector cond_frequency with 292941 elements.
Creating vector time with 292941 elements.
Creating vector temp_frequency with 292941 elements.
Creating vector time with 292941 elements.
Creating vector flow2 with 292941 elements.
Creating vector time with 292941 elements.
Creating vector spare with 292941 elements.
Creating vector time with 292941 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/ctdDriver2.cfg
 
Processing ISUS data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/isuslog.nc')
Creating vector time with 54258 elements.
Creating vector isusNitrate with 54258 elements.
Creating vector time with 54258 elements.
Creating vector isusTemp with 54258 elements.
Creating vector time with 54258 elements.
Creating vector isusQuality with 54258 elements.
Creating vector time with 54258 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/isuslog.nc');
Total lag applied to nitrate = 6 seconds
 
Processing Biolume data...
[Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 75)
  In processBiolume (line 21)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
[Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] 
[> In rmpath (line 75)
  In processBiolume (line 22)
  In processAUVmission (line 220)
  In AUVprocess_main (line 225)] 
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/biolume.nc')
Creating vector time with 73345 elements.
Creating vector rrr with 73345 elements.
Creating vector time with 73345 elements.
Creating vector cal_striing with 73345 elements.
Creating vector time with 73345 elements.
Creating vector pump with 73345 elements.
Creating vector time with 73345 elements.
Creating vector flow with 73345 elements.
Creating vector time with 73345 elements.
Creating vector humidity with 73345 elements.
Creating vector time with 73345 elements.
Creating vector temperature with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_0 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_1 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_2 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_3 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_4 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_5 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_6 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_7 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_8 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_9 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_10 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_11 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_12 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_13 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_14 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_15 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_16 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_17 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_18 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_19 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_20 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_21 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_22 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_23 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_24 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_25 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_26 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_27 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_28 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_29 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_30 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_31 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_32 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_33 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_34 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_35 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_36 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_37 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_38 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_39 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_40 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_41 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_42 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_43 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_44 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_45 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_46 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_47 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_48 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_49 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_50 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_51 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_52 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_53 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_54 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_55 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_56 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_57 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_58 with 73345 elements.
Creating vector time with 73345 elements.
Creating vector raw_59 with 73345 elements.
Creating vector time with 73345 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/biolume.nc');
 
Processing LOPC plankton data...
loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/lopc.nc')
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/lopc.nc.dods?.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/lopc.nc');
Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2007/2007211/2007.211.02/lopc.nc.das.
The OPeNDAP server returned the following message:
Not Found: The data source or server could not be found.
        Often this means that the OPeNDAP server is missing or needs attention;
        Please contact the server administrator.


*** Setting lopc structure to NaNs. *** 
 
save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007.211.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Calling build_auv_survey.m to construct survey file...

SecondaryDissolvedO2 =

     []

Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007.211.02.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 14 segments.
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02.mat
Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02.mat
 
 
*************************************************************************
Calling plot_sections from ../viz to produce section plots ...
Using median boxcar filter of vector...
Using mean boxcar filter of vector...
Number of profiles found = 114 Gridding with nix = 342, iZ = 500
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 359977 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 359977 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 119028 elements.

ds = 

  cfdataset with properties:

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

SWR data read from OPeNDAP has time range: 07/30/2007 12:30  to 07/31/2007 11:30 

swr =

  497.7283
  494.9541
  485.2804
  347.7818
  244.9588
  140.4034
   62.3174
   14.5111
    1.6320
       NaN
       NaN
       NaN
       NaN
       NaN
       NaN
       NaN
       NaN
       NaN
    4.3400
   33.8280
   71.6798
  158.1602
  293.6639
  343.8183

Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02_swr.png
Done plotting SWR.
Executing: /bin/rm -f ../results/2007211_GulperTimes.txt && touch ../results/2007211_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/2007/2007211/2007.211.02/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2007/2007211/2007.211.02/syslog -startEsecs 1185831572.6825 -surveyName Dorado389_2007_211_02_211_02 >> ../results/2007211_GulperTimes.txt
Executing: removeGulpDups.py ../results/2007211_GulperTimes.txt
Bottle: 0 Time: 1185832502.2088 Depth: -0.030293 Dist: 1.0826
Bottle: 1 Time: 1185832559.4049 Depth: 5.6324 Dist: 1.1495
Bottle: 2 Time: 1185832573.014 Depth: 10.9213 Dist: 1.1681
Bottle: 3 Time: 1185832597.2123 Depth: 21.0096 Dist: 1.2031
Bottle: 4 Time: 1185832621.0107 Depth: 31.0514 Dist: 1.2386
Bottle: 5 Time: 1185832645.609 Depth: 41.0897 Dist: 1.2735
Bottle: 6 Time: 1185832692.8058 Depth: 60.9345 Dist: 1.3415
Bottle: 7 Time: 1185832741.2125 Depth: 80.8953 Dist: 1.4123
Bottle: 8 Time: 1185832789.6091 Depth: 100.9726 Dist: 1.4822
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02_gridded.mat

outvarstr =

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

2Column contouring gridded variable gD
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gT
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gS
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gN
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gO
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB470
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gB676
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gF
  Drawing bottom contour from EM300 data
2Column contouring gridded variable gBL
  Drawing bottom contour from EM300 data
Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02_2column.png
Elapsed time to save image: 12 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_211_02_211_02_biolume.png
Elapsed time to save image: 44 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_211_02_211_02_lopc.png
Elapsed time to save image: 11 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_211_02_211_02_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02_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_211_02_211_02_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_211_02_211_02_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_211_02_211_02_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_211_02_211_02_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_211_02_211_02_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_211_02_211_02_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_211_02_211_02_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_211_02_211_02_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_211_02_211_02_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_211_02_211_02_Nitrate.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_211_02_211_02_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_211_02_211_02_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_211_02_211_02_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_211_02_211_02_Optical_Backscatter_470_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_211_02_211_02_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_211_02_211_02_Optical_Backscatter_676_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_211_02_211_02_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_211_02_211_02_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_211_02_211_02_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_211_02_211_02_Bioluminescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_211_02_211_02_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_211_02_211_02_LOPC_Total_Count.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2007_211_02_211_02_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_211_02_211_02.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02.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_211_02_211_02_LOPC_Total_Count.kml'
not found.] 
[> In create_data_products (line 414)
  In build_auv_survey (line 522)
  In AUVprocess_main (line 255)] 
 
 
*************************************************************************
Writing ODV file ...
Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02.mat ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
6 NaNs found in bbpRed.  Interpolating anyway.
Encountered 905 NaN values in array of lon that is 54244 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 53339 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 53339 are not equal to number of Lat lon points = 54244
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_211_02_211_02.txt
Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007_211_02_211_02.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_211_02_211_02_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2007/odv/.  Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to isus time values...
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
6 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_211_02_211_02_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_211_02_211_02.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_211_02_211_02_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_211_02_211_02.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_211_02_211_02 processed" mccann@mbari.org < mail_Dorado389_2007_211_02_211_02.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2007.211.02.mat
Processing time: 672 seconds