Execution of AUVprocess_main version 1.87 at 2018-08-11T01:25:03Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2010, ['154.01'], '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: 2010.154.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/navigation.nc') Creating vector time with 214458 elements. Creating vector mPos_x with 214458 elements. Creating vector time with 214458 elements. Creating vector mPos_y with 214458 elements. Creating vector time with 214458 elements. Creating vector mDepth with 214458 elements. Creating vector time with 214458 elements. Creating vector mGpsNorth with 214458 elements. Creating vector time with 214458 elements. Creating vector mGpsEast with 214458 elements. Creating vector time with 214458 elements. Creating vector mGpsValid with 214458 elements. Creating vector time with 214458 elements. Creating vector mPhi with 214458 elements. Creating vector time with 214458 elements. Creating vector mTheta with 214458 elements. Creating vector time with 214458 elements. Creating vector mPsi with 214458 elements. Creating vector time with 214458 elements. Creating vector mOmega_x with 214458 elements. Creating vector time with 214458 elements. Creating vector mOmega_y with 214458 elements. Creating vector time with 214458 elements. Creating vector mOmega_z with 214458 elements. Creating vector time with 214458 elements. Creating vector mPsaRange with 214458 elements. Creating vector time with 214458 elements. Creating vector mAltitude with 214458 elements. Creating vector time with 214458 elements. Creating vector mDvlAltitude with 214458 elements. Creating vector time with 214458 elements. Creating vector mWaterSpeed with 214458 elements. Creating vector time with 214458 elements. Creating vector mDvlValid with 214458 elements. Creating vector time with 214458 elements. Creating vector mDvlNewData with 214458 elements. Creating vector time with 214458 elements. Creating vector mDeltaT with 214458 elements. Creating vector time with 214458 elements. Creating vector nfix with 214458 elements. Creating vector time with 214458 elements. Creating vector efix with 214458 elements. Creating vector time with 214458 elements. Creating vector filter_north with 214458 elements. Creating vector time with 214458 elements. Creating vector filter_east with 214458 elements. Creating vector time with 214458 elements. Creating vector filter_depth with 214458 elements. Creating vector time with 214458 elements. Creating vector north_current with 214458 elements. Creating vector time with 214458 elements. Creating vector east_current with 214458 elements. Creating vector time with 214458 elements. Creating vector speed_bias with 214458 elements. Creating vector time with 214458 elements. Creating vector heading_bias with 214458 elements. Creating vector time with 214458 elements. Creating vector latitude with 214458 elements. Creating vector time with 214458 elements. Creating vector longitude with 214458 elements. Creating vector time with 214458 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/navigation.nc'); processNav(): median of positive valued depths = 688.3837 processNav(): Finding depths less than 4818.6861 and times > 0 processNav(): length(Nav.depth) = 214458 processNav(): length(gindx) = 214458 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/2010/2010154/2010.154.01/gps.nc') Creating vector time with 1577 elements. Creating vector hours with 1577 elements. Creating vector time with 1577 elements. Creating vector minutes with 1577 elements. Creating vector time with 1577 elements. Creating vector seconds with 1577 elements. Creating vector time with 1577 elements. Creating vector centiSeconds with 1577 elements. Creating vector time with 1577 elements. Creating vector latitude with 1577 elements. Creating vector time with 1577 elements. Creating vector longitude with 1577 elements. Creating vector time with 1577 elements. Creating vector quality with 1577 elements. Creating vector time with 1577 elements. Creating vector numberOfSatellites with 1577 elements. Creating vector time with 1577 elements. Creating vector hdop with 1577 elements. Creating vector time with 1577 elements. Creating vector antennaHeight with 1577 elements. Creating vector time with 1577 elements. Creating vector geoHeight with 1577 elements. Creating vector time with 1577 elements. Creating vector dgpsDataAge with 1577 elements. Creating vector time with 1577 elements. Creating vector dgpsRSID with 1577 elements. Creating vector time with 1577 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/parosci.nc') Creating vector time with 351726 elements. Creating vector depth with 351726 elements. Creating vector time with 351726 elements. Creating vector temp with 351726 elements. Creating vector time with 351726 elements. Creating vector pressure with 351726 elements. Creating vector time with 351726 elements. Creating vector temp_period with 351726 elements. Creating vector time with 351726 elements. Creating vector pres_period with 351726 elements. Creating vector time with 351726 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -1.0557 max(Depth.data) = 1201.202 Found 231805 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.99987 max(Depth.data) = 299.9943 [Warning: P-file /mbari/matlab/toolbox/matlab/ops/unique.p is older than MATLAB file /mbari/matlab/toolbox/matlab/ops/unique.m. /mbari/matlab/toolbox/matlab/ops/unique.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In fix_depth_time (line 6) In processDepth (line 65) In processAUVmission (line 106) In AUVprocess_main (line 225)] 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/2010/2010154/2010.154.01/hydroscatlog.nc') Creating vector time with 171593 elements. Creating vector Seconds with 171593 elements. Creating vector time with 171593 elements. Creating vector HundrethsOfSeconds with 171593 elements. Creating vector time with 171593 elements. Creating vector Snorm1 with 171593 elements. Creating vector time with 171593 elements. Creating vector Snorm2 with 171593 elements. Creating vector time with 171593 elements. Creating vector Snorm3 with 171593 elements. Creating vector time with 171593 elements. Creating vector Gain_Status_1 with 171593 elements. Creating vector time with 171593 elements. Creating vector Gain_Status_2 with 171593 elements. Creating vector time with 171593 elements. Creating vector Gain_Status_3 with 171593 elements. Creating vector time with 171593 elements. Creating vector RawDepthValue with 171593 elements. Creating vector time with 171593 elements. Creating vector RawTempValue with 171593 elements. Creating vector time with 171593 elements. Creating vector Temperature with 171593 elements. Creating vector time with 171593 elements. Creating vector ErrorValue with 171593 elements. Creating vector time with 171593 elements. Creating vector bb470 with 171593 elements. Creating vector time with 171593 elements. Creating vector bb676 with 171593 elements. Creating vector time with 171593 elements. Creating vector fl676u with 171593 elements. Creating vector time with 171593 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/ctdDriver.nc') Creating vector time with 171624 elements. Creating vector conductivity with 171624 elements. Creating vector time with 171624 elements. Creating vector temperature with 171624 elements. Creating vector time with 171624 elements. Creating vector cond_frequency with 171624 elements. Creating vector time with 171624 elements. Creating vector temp_frequency with 171624 elements. Creating vector time with 171624 elements. Creating vector spare with 171624 elements. Creating vector time with 171624 elements. Creating vector humidity with 171624 elements. Creating vector time with 171624 elements. Creating vector flow1 with 171624 elements. Creating vector time with 171624 elements. Creating vector CDOM with 171624 elements. Creating vector time with 171624 elements. Creating vector dissolvedO2 with 171624 elements. Creating vector time with 171624 elements. Creating vector salinity with 171624 elements. Creating vector time with 171624 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/ctdDriver2.nc') Creating vector time with 171464 elements. Creating vector conductivity with 171464 elements. Creating vector time with 171464 elements. Creating vector temperature with 171464 elements. Creating vector time with 171464 elements. Creating vector cond_frequency with 171464 elements. Creating vector time with 171464 elements. Creating vector temp_frequency with 171464 elements. Creating vector time with 171464 elements. Creating vector flow2 with 171464 elements. Creating vector time with 171464 elements. Creating vector spare with 171464 elements. Creating vector time with 171464 elements. Creating vector salinity with 171464 elements. Creating vector time with 171464 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/isuslog.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/2010/2010154/2010.154.01/isuslog.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/2010/2010154/2010.154.01/isuslog.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/2010/2010154/2010.154.01/isuslog.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 ISUS structure to NaN values. 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/2010/2010154/2010.154.01/biolume.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/2010/2010154/2010.154.01/biolume.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/2010/2010154/2010.154.01/biolume.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/2010/2010154/2010.154.01/biolume.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. Could not read from biolume.nc returning NaNs for fields. 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/2010/2010154/2010.154.01/lopc.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/lopc.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/lopc.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010154/2010.154.01/lopc.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.154.01.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_2010.154.01.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 4 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_nav_adjust.png [Warning: P-file /mbari/matlab/toolbox/matlab/imagesci/imformats.p is older than MATLAB file /mbari/matlab/toolbox/matlab/imagesci/imformats.m. /mbari/matlab/toolbox/matlab/imagesci/imformats.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In imwrite>parse_inputs (line 557) In imwrite (line 418) In writeRaster In printingGenerateOutput In alternatePrintPath In print (line 82) In create_data_products (line 99) In build_auv_survey (line 522) In AUVprocess_main (line 255)] [Warning: P-file /mbari/matlab/toolbox/matlab/timefun/datevec.p is older than MATLAB file /mbari/matlab/toolbox/matlab/timefun/datevec.m. /mbari/matlab/toolbox/matlab/timefun/datevec.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In datenum (line 103) In writepng (line 232) In imwrite (line 485) In writeRaster In printingGenerateOutput In alternatePrintPath In print (line 82) In create_data_products (line 99) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01.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 = 36 Gridding with nix = 108, iZ = 2406 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 Only one good point - NaNing the gN array. BL Only one good point or fewer - NaNing the gBL array. BLflow Only one good point or fewer - NaNing the gBLflow array. 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 No valid data for gN cvarname = gF cvarname = gB470 cvarname = gB676 cvarname = gBL No valid data for gBL cvarname = gBLflow No valid data for 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 214404 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 f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Some input points were outside the grid domain(s). grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447) No depth array returned by grdtrack. Perhaps grdtrack could not be found in the search path. Setting ocean depths to 4000m for the track. Executing: /bin/rm -f ../results/2010154_GulperTimes.txt && touch ../results/2010154_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/2010/2010154/2010.154.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010154/2010.154.01/syslog -startEsecs 1275566159.2083 -surveyName Dorado389_2010_154_01_154_01 >> ../results/2010154_GulperTimes.txt Executing: removeGulpDups.py ../results/2010154_GulperTimes.txt Bottle: 0 Time: 1275572533 Depth: 1182.5426 Dist: 7.2728 Bottle: 1 Time: 1275573421 Depth: 1129.5148 Dist: 8.4231 Bottle: 2 Time: 1275577611 Depth: 1198.1138 Dist: 12.2142 Bottle: 3 Time: 1275578439 Depth: 1193.6582 Dist: 13.1946 Bottle: 4 Time: 1275582788 Depth: 1179.4227 Dist: 17.494 Bottle: 5 Time: 1275583586 Depth: 1194.0846 Dist: 18.5231 Bottle: 6 Time: 1275588092 Depth: 1096.4237 Dist: 22.6585 Bottle: 7 Time: 1275588778 Depth: 1196.3511 Dist: 23.4557 Bottle: 8 Time: 1275593225 Depth: 1174.9074 Dist: 27.4177 Bottle: 9 Time: 1275594039 Depth: 1173.8228 Dist: 28.4684 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_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 Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_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 Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_biolume.png Elapsed time to save image: 20 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 Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_lopc.png Elapsed time to save image: 5 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... [Warning: P-file /mbari/matlab/toolbox/matlab/graph2d/subplot.p is older than MATLAB file /mbari/matlab/toolbox/matlab/graph2d/subplot.m. /mbari/matlab/toolbox/matlab/graph2d/subplot.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In plot_survey_stats (line 47) In create_data_products (line 134) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_2column.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_biolume.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_lopc.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2010/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_2010_154_01_154_01_Temperature.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_154_01_154_01_Salinity.kml (deflated 95%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2010/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); length(v_esecs(gindx)) = which is less than 2. Not processing. adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_Nitrate.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_154_01_154_01_Oxygen.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_154_01_154_01_Optical_Backscatter_470_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_Optical_Backscatter_470_nm.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_154_01_154_01_Optical_Backscatter_676_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_Optical_Backscatter_676_nm.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_154_01_154_01_Chlorophyll_Fluorescence.kml (deflated 95%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2010/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); length(v_esecs(gindx)) = which is less than 2. Not processing. adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_Bioluminescence.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2010/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_2010_154_01_154_01_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2010_154_01_154_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01.kml... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_154_01_154_01_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 420) 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_2010_154_01_154_01.mat ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 122 NaNs found in bbpBlue. Interpolating anyway. 95 NaNs found in bbpRed. Interpolating anyway. 36 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 0 NaN values in array of lon that is 17163 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 f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Some input points were outside the grid domain(s). grdtrack: Sampled 0 points from grid Monterey25.grd (2876 x 2447) No depth array returned by grdtrack. Setting bottom depth to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01.txt... Copied to /mbari/AUVCTD/surveys/2010/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2010/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to 2 second increments between Nav time bounds... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 122 NaNs found in bbpBlue. Interpolating anyway. 95 NaNs found in bbpRed. Interpolating anyway. 36 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_2010_154_01_154_01_decim.nc... Copied to /mbari/AUVCTD/surveys/2010/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_2010_154_01_154_01.nc... Copied to /mbari/AUVCTD/surveys/2010/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01_gridded.mat... Copied to /mbari/AUVCTD/surveys/2010/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_154_01_154_01.mat... Copied to /mbari/AUVCTD/surveys/2010/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2010_154_01_154_01 processed" mccann@mbari.org < mail_Dorado389_2010_154_01_154_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.154.01.mat Processing time: 114 seconds