Execution of AUVprocess_main version 1.85 at 2014-03-18T06:21:45Z on elvis Matlab command executed: AUVprocess_main('BIOLUME', 2006, ['214.01'], '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: 2006.214.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/ 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/2006/2006214/2006.214.01/navigation.nc') Creating vector time with 215508 elements. Creating vector mPos_x with 215508 elements. Creating vector time with 215508 elements. Creating vector mPos_y with 215508 elements. Creating vector time with 215508 elements. Creating vector mDepth with 215508 elements. Creating vector time with 215508 elements. Creating vector mGpsNorth with 215508 elements. Creating vector time with 215508 elements. Creating vector mGpsEast with 215508 elements. Creating vector time with 215508 elements. Creating vector mGpsValid with 215508 elements. Creating vector time with 215508 elements. Creating vector mPhi with 215508 elements. Creating vector time with 215508 elements. Creating vector mTheta with 215508 elements. Creating vector time with 215508 elements. Creating vector mPsi with 215508 elements. Creating vector time with 215508 elements. Creating vector mOmega_x with 215508 elements. Creating vector time with 215508 elements. Creating vector mOmega_y with 215508 elements. Creating vector time with 215508 elements. Creating vector mOmega_z with 215508 elements. Creating vector time with 215508 elements. Creating vector mPsaRange with 215508 elements. Creating vector time with 215508 elements. Creating vector mAltitude with 215508 elements. Creating vector time with 215508 elements. Creating vector mDvlAltitude with 215508 elements. Creating vector time with 215508 elements. Creating vector mWaterSpeed with 215508 elements. Creating vector time with 215508 elements. Creating vector mDvlValid with 215508 elements. Creating vector time with 215508 elements. Creating vector mDvlNewData with 215508 elements. Creating vector time with 215508 elements. Creating vector mDeltaT with 215508 elements. Creating vector time with 215508 elements. Creating vector nfix with 215508 elements. Creating vector time with 215508 elements. Creating vector efix with 215508 elements. Creating vector time with 215508 elements. Creating vector filter_north with 215508 elements. Creating vector time with 215508 elements. Creating vector filter_east with 215508 elements. Creating vector time with 215508 elements. Creating vector filter_depth with 215508 elements. Creating vector time with 215508 elements. Creating vector north_current with 215508 elements. Creating vector time with 215508 elements. Creating vector east_current with 215508 elements. Creating vector time with 215508 elements. Creating vector speed_bias with 215508 elements. Creating vector time with 215508 elements. Creating vector heading_bias with 215508 elements. Creating vector time with 215508 elements. Creating vector latitude with 215508 elements. Creating vector time with 215508 elements. Creating vector longitude with 215508 elements. Creating vector time with 215508 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/navigation.nc'); processNav(): median of positive valued depths = 13.7488 processNav(): Finding depths less than 68.7438 and times > 0 processNav(): length(Nav.depth) = 215508 processNav(): length(gindx) = 195489 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/2006/2006214/2006.214.01/gps.nc') Creating vector time with 1056 elements. Creating vector hours with 1056 elements. Creating vector time with 1056 elements. Creating vector minutes with 1056 elements. Creating vector time with 1056 elements. Creating vector seconds with 1056 elements. Creating vector time with 1056 elements. Creating vector centiSeconds with 1056 elements. Creating vector time with 1056 elements. Creating vector latitude with 1056 elements. Creating vector time with 1056 elements. Creating vector longitude with 1056 elements. Creating vector time with 1056 elements. Creating vector quality with 1056 elements. Creating vector time with 1056 elements. Creating vector numberOfSatellites with 1056 elements. Creating vector time with 1056 elements. Creating vector hdop with 1056 elements. Creating vector time with 1056 elements. Creating vector antennaHeight with 1056 elements. Creating vector time with 1056 elements. Creating vector geoHeight with 1056 elements. Creating vector time with 1056 elements. Creating vector dgpsDataAge with 1056 elements. Creating vector time with 1056 elements. Creating vector dgpsRSID with 1056 elements. Creating vector time with 1056 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/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/2006/2006214/2006.214.01/parosci.nc') Creating vector time with 460899 elements. Creating vector depth with 460899 elements. Creating vector time with 460899 elements. Creating vector temp with 460899 elements. Creating vector time with 460899 elements. Creating vector pressure with 460899 elements. Creating vector time with 460899 elements. Creating vector temp_period with 460899 elements. Creating vector time with 460899 elements. Creating vector pres_period with 460899 elements. Creating vector time with 460899 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.11306 max(Depth.data) = 100.3798 Found 1652 bad (> 300 | < 0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = 4.0014e-05 max(Depth.data) = 100.3798 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/2006/2006214/2006.214.01/hydroscatlog.nc') Creating vector time with 172431 elements. Creating vector Seconds with 172431 elements. Creating vector time with 172431 elements. Creating vector HundrethsOfSeconds with 172431 elements. Creating vector time with 172431 elements. Creating vector Snorm1 with 172431 elements. Creating vector time with 172431 elements. Creating vector Snorm2 with 172431 elements. Creating vector time with 172431 elements. Creating vector Snorm3 with 172431 elements. Creating vector time with 172431 elements. Creating vector Gain_Status_1 with 172431 elements. Creating vector time with 172431 elements. Creating vector Gain_Status_2 with 172431 elements. Creating vector time with 172431 elements. Creating vector Gain_Status_3 with 172431 elements. Creating vector time with 172431 elements. Creating vector RawDepthValue with 172431 elements. Creating vector time with 172431 elements. Creating vector RawTempValue with 172431 elements. Creating vector time with 172431 elements. Creating vector Temperature with 172431 elements. Creating vector time with 172431 elements. Creating vector ErrorValue with 172431 elements. Creating vector time with 172431 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/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/2006/2006214/2006.214.01/ctdDriver.nc') Creating vector time with 172376 elements. Creating vector conductivity with 172376 elements. Creating vector time with 172376 elements. Creating vector temperature with 172376 elements. Creating vector time with 172376 elements. Creating vector cond_frequency with 172376 elements. Creating vector time with 172376 elements. Creating vector temp_frequency with 172376 elements. Creating vector time with 172376 elements. Creating vector spare with 172376 elements. Creating vector time with 172376 elements. Creating vector humidity with 172376 elements. Creating vector time with 172376 elements. Creating vector flow1 with 172376 elements. Creating vector time with 172376 elements. Creating vector OBS with 172376 elements. Creating vector time with 172376 elements. Creating vector dissolvedO2 with 172376 elements. Creating vector time with 172376 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/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/2006/2006214/2006.214.01/ctdDriver2.nc') Creating vector time with 172364 elements. Creating vector conductivity with 172364 elements. Creating vector time with 172364 elements. Creating vector temperature with 172364 elements. Creating vector time with 172364 elements. Creating vector cond_frequency with 172364 elements. Creating vector time with 172364 elements. Creating vector temp_frequency with 172364 elements. Creating vector time with 172364 elements. Creating vector flow2 with 172364 elements. Creating vector time with 172364 elements. Creating vector spare with 172364 elements. Creating vector time with 172364 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/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/2006/2006214/2006.214.01/isuslog.nc') Creating vector time with 32397 elements. Creating vector isusNitrate with 32397 elements. Creating vector time with 32397 elements. Creating vector isusTemp with 32397 elements. Creating vector time with 32397 elements. Creating vector isusQuality with 32397 elements. Creating vector time with 32397 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... {Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.} {> In rmpath at 58 In processBiolume at 21 In processAUVmission at 220 In AUVprocess_main at 220 In reprocess_surveys at 578} loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/biolume.nc') Creating vector time with 43136 elements. Creating vector rrr with 43136 elements. Creating vector time with 43136 elements. Creating vector cal_striing with 43136 elements. Creating vector time with 43136 elements. Creating vector pump with 43136 elements. Creating vector time with 43136 elements. Creating vector flow with 43136 elements. Creating vector time with 43136 elements. Creating vector humidity with 43136 elements. Creating vector time with 43136 elements. Creating vector temperature with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_0 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_1 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_2 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_3 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_4 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_5 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_6 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_7 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_8 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_9 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_10 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_11 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_12 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_13 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_14 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_15 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_16 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_17 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_18 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_19 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_20 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_21 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_22 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_23 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_24 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_25 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_26 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_27 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_28 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_29 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_30 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_31 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_32 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_33 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_34 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_35 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_36 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_37 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_38 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_39 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_40 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_41 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_42 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_43 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_44 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_45 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_46 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_47 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_48 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_49 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_50 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_51 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_52 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_53 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_54 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_55 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_56 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_57 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_58 with 43136 elements. Creating vector time with 43136 elements. Creating vector raw_59 with 43136 elements. Creating vector time with 43136 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/biolume.nc'); Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2006/2006214/2006.214.01/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/2006/2006214/2006.214.01/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/2006/2006214/2006.214.01/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/2006/2006214/2006.214.01/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_2006.214.01.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_2006.214.01.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 17 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_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 = 476 Gridding with nix = 1428, iZ = 134 Using mean boxcar filter of vector... Using mean boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Gridding... T S O Using median boxcar filter of vector... Using median boxcar filter of vector... Using median boxcar filter of vector... bbp470 {Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.} {> In griddata>linear at 205 In griddata at 125 In plot_sections at 230 In create_data_products at 119 In build_auv_survey at 497 In AUVprocess_main at 250 In reprocess_surveys at 578} bbp676 {Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.} {> In griddata>linear at 205 In griddata at 125 In plot_sections at 252 In create_data_products at 119 In build_auv_survey at 497 In AUVprocess_main at 250 In reprocess_surveys at 578} fl676_uncorr {Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.} {> In griddata>linear at 205 In griddata at 125 In plot_sections at 273 In create_data_products at 119 In build_auv_survey at 497 In AUVprocess_main at 250 In reprocess_surveys at 578} N BL BLflow Maximum idx exceedes size of biolume.flow - 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 cvarname = gF cvarname = gB470 cvarname = gB676 cvarname = 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 195320 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 195320 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[15568:1:15582][0:1:0][0:1:0][0:1:0] Creating matrix SW (15 x 1 x 1 x 1) with 15 elements. Creating vector TIME with 15 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: 08/01/2006 19:29 to 08/02/2006 09:30 swr = 20.9622 1.5000 0 0 0.1000 0 0 0 0 0 0 6.7351 33.9412 84.5181 164.8111 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2006214_GulperTimes.txt && touch ../results/2006214_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/2006/2006214/2006.214.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2006/2006214/2006.214.01/syslog -startEsecs 1154489007.2964 -surveyName Dorado389_2006_214_01_214_01 >> ../results/2006214_GulperTimes.txt Executing: perl removeGulpDups.pl ../results/2006214_GulperTimes.txt Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_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 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_2006_214_01_214_01_2column.png Elapsed time to save image: 4 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_2006_214_01_214_01_biolume.png Elapsed time to save image: 24 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_2006_214_01_214_01_lopc.png Elapsed time to save image: 4 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_2006_214_01_214_01_hist_stats.png {Warning: Imaginary parts of complex X and/or Y arguments ignored} {> In plot_survey_stats at 124 In create_data_products at 128 In build_auv_survey at 497 In AUVprocess_main at 250 In reprocess_surveys at 578} Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_2column.png... Copied to /mbari/AUVCTD/surveys/2006/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_biolume.png... Copied to /mbari/AUVCTD/surveys/2006/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_lopc.png... Copied to /mbari/AUVCTD/surveys/2006/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2006/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2006/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2006/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_2006_214_01_214_01_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_214_01_214_01_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2006/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_2006_214_01_214_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_214_01_214_01_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2006/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_2006_214_01_214_01_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_214_01_214_01_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2006/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_2006_214_01_214_01_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_214_01_214_01_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2006/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @470 nm', jetplus, varlimits(5,:), hs2.bbp470, time.hs2, auvnav, depth.hs2, resultspath); Could not do interp1: The point coordinates are not sequenced in strict monotonic order. Did not write KML for this variable. Rethrowing error. Could not create .kmz for Optical Backscatter @470 nm KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath); Could not do interp1: The point coordinates are not sequenced in strict monotonic order. Did not write KML for this variable. Rethrowing error. Could not create .kmz for Optical Backscatter @676 nm KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath); Could not do interp1: The point coordinates are not sequenced in strict monotonic order. Did not write KML for this variable. Rethrowing error. Could not create .kmz for Chlorophyll Fluorescence KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_214_01_214_01_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_214_01_214_01_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2006/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_2006_214_01_214_01_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_214_01_214_01_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2006/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2006_214_01_214_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01.kml... Copied to /mbari/AUVCTD/surveys/2006/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ {Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2006_214_01_214_01_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 578} ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Encountered 26 NaN values in array of lon that is 32397 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 32371 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 32371 are not equal to number of Lat lon points = 32397 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_2006_214_01_214_01.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01.txt... Copied to /mbari/AUVCTD/surveys/2006/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_Gulper.txt... Tried, but failed to copy to /mbari/AUVCTD/surveys/2006/odv/ cp: cannot stat `/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_Gulper.txt': No such file or directory ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_decim.nc... Copied to /mbari/AUVCTD/surveys/2006/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_2006_214_01_214_01.nc... Copied to /mbari/AUVCTD/surveys/2006/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01_gridded.mat... Copied to /mbari/AUVCTD/surveys/2006/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006_214_01_214_01.mat... Copied to /mbari/AUVCTD/surveys/2006/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2006_214_01_214_01 processed" mccann@mbari.org < mail_Dorado389_2006_214_01_214_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2006.214.01.mat Processing time: 247 seconds