Execution of AUVprocess_main version 1.86 at 2018-05-23T23:09:11Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2011, ['060.01'], '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: 2011.060.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/ 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/2011/2011060/2011.060.01/navigation.nc') Creating vector time with 42782 elements. Creating vector mPos_x with 42782 elements. Creating vector time with 42782 elements. Creating vector mPos_y with 42782 elements. Creating vector time with 42782 elements. Creating vector mDepth with 42782 elements. Creating vector time with 42782 elements. Creating vector mGpsNorth with 42782 elements. Creating vector time with 42782 elements. Creating vector mGpsEast with 42782 elements. Creating vector time with 42782 elements. Creating vector mGpsValid with 42782 elements. Creating vector time with 42782 elements. Creating vector mPhi with 42782 elements. Creating vector time with 42782 elements. Creating vector mTheta with 42782 elements. Creating vector time with 42782 elements. Creating vector mPsi with 42782 elements. Creating vector time with 42782 elements. Creating vector mOmega_x with 42782 elements. Creating vector time with 42782 elements. Creating vector mOmega_y with 42782 elements. Creating vector time with 42782 elements. Creating vector mOmega_z with 42782 elements. Creating vector time with 42782 elements. Creating vector mPsaRange with 42782 elements. Creating vector time with 42782 elements. Creating vector mAltitude with 42782 elements. Creating vector time with 42782 elements. Creating vector mDvlAltitude with 42782 elements. Creating vector time with 42782 elements. Creating vector mWaterSpeed with 42782 elements. Creating vector time with 42782 elements. Creating vector mDvlValid with 42782 elements. Creating vector time with 42782 elements. Creating vector mDvlNewData with 42782 elements. Creating vector time with 42782 elements. Creating vector mDeltaT with 42782 elements. Creating vector time with 42782 elements. Creating vector nfix with 42782 elements. Creating vector time with 42782 elements. Creating vector efix with 42782 elements. Creating vector time with 42782 elements. Creating vector filter_north with 42782 elements. Creating vector time with 42782 elements. Creating vector filter_east with 42782 elements. Creating vector time with 42782 elements. Creating vector filter_depth with 42782 elements. Creating vector time with 42782 elements. Creating vector north_current with 42782 elements. Creating vector time with 42782 elements. Creating vector east_current with 42782 elements. Creating vector time with 42782 elements. Creating vector speed_bias with 42782 elements. Creating vector time with 42782 elements. Creating vector heading_bias with 42782 elements. Creating vector time with 42782 elements. Creating vector latitude with 42782 elements. Creating vector time with 42782 elements. Creating vector longitude with 42782 elements. Creating vector time with 42782 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/navigation.nc'); [Warning: P-file /mbari/matlab/toolbox/matlab/strfun/num2str.p is older than MATLAB file /mbari/matlab/toolbox/matlab/strfun/num2str.m. /mbari/matlab/toolbox/matlab/strfun/num2str.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In processNav (line 62) In processAUVmission (line 60) In AUVprocess_main (line 225)] processNav(): median of positive valued depths = 21.1792 processNav(): Finding depths less than 148.2542 and times > 0 processNav(): length(Nav.depth) = 42782 processNav(): length(gindx) = 42782 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/2011/2011060/2011.060.01/gps.nc') Creating vector time with 2352 elements. Creating vector hours with 2352 elements. Creating vector time with 2352 elements. Creating vector minutes with 2352 elements. Creating vector time with 2352 elements. Creating vector seconds with 2352 elements. Creating vector time with 2352 elements. Creating vector centiSeconds with 2352 elements. Creating vector time with 2352 elements. Creating vector latitude with 2352 elements. Creating vector time with 2352 elements. Creating vector longitude with 2352 elements. Creating vector time with 2352 elements. Creating vector quality with 2352 elements. Creating vector time with 2352 elements. Creating vector numberOfSatellites with 2352 elements. Creating vector time with 2352 elements. Creating vector hdop with 2352 elements. Creating vector time with 2352 elements. Creating vector antennaHeight with 2352 elements. Creating vector time with 2352 elements. Creating vector geoHeight with 2352 elements. Creating vector time with 2352 elements. Creating vector dgpsDataAge with 2352 elements. Creating vector time with 2352 elements. Creating vector dgpsRSID with 2352 elements. Creating vector time with 2352 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/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/2011/2011060/2011.060.01/parosci.nc') Creating vector time with 72974 elements. Creating vector depth with 72974 elements. Creating vector time with 72974 elements. Creating vector temp with 72974 elements. Creating vector time with 72974 elements. Creating vector pressure with 72974 elements. Creating vector time with 72974 elements. Creating vector temp_period with 72974 elements. Creating vector time with 72974 elements. Creating vector pres_period with 72974 elements. Creating vector time with 72974 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.16159 max(Depth.data) = 40.225 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.16159 max(Depth.data) = 40.225 [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/2011/2011060/2011.060.01/hydroscatlog.nc') Creating vector time with 34389 elements. Creating vector Seconds with 34389 elements. Creating vector time with 34389 elements. Creating vector HundrethsOfSeconds with 34389 elements. Creating vector time with 34389 elements. Creating vector Snorm1 with 34389 elements. Creating vector time with 34389 elements. Creating vector Snorm2 with 34389 elements. Creating vector time with 34389 elements. Creating vector Snorm3 with 34389 elements. Creating vector time with 34389 elements. Creating vector Gain_Status_1 with 34389 elements. Creating vector time with 34389 elements. Creating vector Gain_Status_2 with 34389 elements. Creating vector time with 34389 elements. Creating vector Gain_Status_3 with 34389 elements. Creating vector time with 34389 elements. Creating vector RawDepthValue with 34389 elements. Creating vector time with 34389 elements. Creating vector RawTempValue with 34389 elements. Creating vector time with 34389 elements. Creating vector Temperature with 34389 elements. Creating vector time with 34389 elements. Creating vector ErrorValue with 34389 elements. Creating vector time with 34389 elements. Creating vector bb470 with 34389 elements. Creating vector time with 34389 elements. Creating vector bb676 with 34389 elements. Creating vector time with 34389 elements. Creating vector fl676u with 34389 elements. Creating vector time with 34389 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/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/2011/2011060/2011.060.01/ctdDriver.nc') Creating vector time with 34316 elements. Creating vector conductivity with 34316 elements. Creating vector time with 34316 elements. Creating vector temperature with 34316 elements. Creating vector time with 34316 elements. Creating vector cond_frequency with 34316 elements. Creating vector time with 34316 elements. Creating vector temp_frequency with 34316 elements. Creating vector time with 34316 elements. Creating vector spare with 34316 elements. Creating vector time with 34316 elements. Creating vector humidity with 34316 elements. Creating vector time with 34316 elements. Creating vector flow1 with 34316 elements. Creating vector time with 34316 elements. Creating vector rhodamine with 34316 elements. Creating vector time with 34316 elements. Creating vector dissolvedO2 with 34316 elements. Creating vector time with 34316 elements. Creating vector salinity with 34316 elements. Creating vector time with 34316 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/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/2011/2011060/2011.060.01/ctdDriver2.nc') Creating vector time with 34316 elements. Creating vector conductivity with 34316 elements. Creating vector time with 34316 elements. Creating vector temperature with 34316 elements. Creating vector time with 34316 elements. Creating vector cond_frequency with 34316 elements. Creating vector time with 34316 elements. Creating vector temp_frequency with 34316 elements. Creating vector time with 34316 elements. Creating vector flow2 with 34316 elements. Creating vector time with 34316 elements. Creating vector spare with 34316 elements. Creating vector time with 34316 elements. Creating vector salinity with 34316 elements. Creating vector time with 34316 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/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/2011/2011060/2011.060.01/isuslog.nc') Creating vector time with 6625 elements. Creating vector isusNitrate with 6625 elements. Creating vector time with 6625 elements. Creating vector isusTemp with 6625 elements. Creating vector time with 6625 elements. Creating vector isusQuality with 6625 elements. Creating vector time with 6625 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (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/2011/2011060/2011.060.01/biolume.nc') Creating vector time with 8463 elements. Creating vector rrr with 8463 elements. Creating vector time with 8463 elements. Creating vector cal_striing with 8463 elements. Creating vector time with 8463 elements. Creating vector avg_biolume with 8463 elements. Creating vector time with 8463 elements. Creating vector pump with 8463 elements. Creating vector time with 8463 elements. Creating vector system_voltage with 8463 elements. Creating vector time with 8463 elements. Creating vector flow with 8463 elements. Creating vector time with 8463 elements. Creating vector HV with 8463 elements. Creating vector time with 8463 elements. Creating vector reserved with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_0 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_1 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_2 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_3 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_4 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_5 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_6 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_7 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_8 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_9 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_10 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_11 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_12 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_13 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_14 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_15 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_16 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_17 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_18 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_19 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_20 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_21 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_22 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_23 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_24 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_25 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_26 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_27 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_28 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_29 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_30 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_31 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_32 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_33 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_34 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_35 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_36 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_37 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_38 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_39 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_40 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_41 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_42 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_43 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_44 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_45 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_46 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_47 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_48 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_49 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_50 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_51 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_52 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_53 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_54 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_55 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_56 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_57 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_58 with 8463 elements. Creating vector time with 8463 elements. Creating vector raw_59 with 8463 elements. Creating vector time with 8463 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/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/2011/2011060/2011.060.01/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (819 x 994) with 814086 elements. Creating vector time with 819 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (819 x 994) with 814086 elements. Creating vector time with 819 elements. Creating vector bin with 994 elements. Creating matrix countList (819 x 994) with 814086 elements. Creating vector time with 819 elements. Creating vector bin with 994 elements. Creating vector LCcount with 819 elements. Creating vector time with 819 elements. Creating vector transCount with 819 elements. Creating vector time with 819 elements. Creating vector nonTransCount with 819 elements. Creating vector time with 819 elements. Creating vector ai_mean with 819 elements. Creating vector time with 819 elements. Creating vector ai_min with 819 elements. Creating vector time with 819 elements. Creating vector ai_max with 819 elements. Creating vector time with 819 elements. Creating vector ai_std with 819 elements. Creating vector time with 819 elements. Creating vector esd_mean with 819 elements. Creating vector time with 819 elements. Creating vector esd_min with 819 elements. Creating vector time with 819 elements. Creating vector esd_max with 819 elements. Creating vector time with 819 elements. Creating vector esd_std with 819 elements. Creating vector time with 819 elements. Creating vector countSum with 819 elements. Creating vector time with 819 elements. Creating vector snapshot with 819 elements. Creating vector time with 819 elements. Creating vector threshold with 819 elements. Creating vector time with 819 elements. Creating vector sampleCount with 819 elements. Creating vector time with 819 elements. Creating vector flowCount with 819 elements. Creating vector time with 819 elements. Creating vector flowTime with 819 elements. Creating vector time with 819 elements. Creating vector bufferStatus with 819 elements. Creating vector time with 819 elements. Creating vector laserLevel with 819 elements. Creating vector time with 819 elements. Creating vector counter with 819 elements. Creating vector time with 819 elements. Creating vector counterPeriod with 819 elements. Creating vector time with 819 elements. Creating vector laserControl with 819 elements. Creating vector time with 819 elements. Creating vector countUnknownFrameCharacter with 819 elements. Creating vector time with 819 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 819 elements. Creating vector time with 819 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 819 elements. Creating vector time with 819 elements. Creating vector flowSpeed with 819 elements. Creating vector time with 819 elements. Creating vector countShortLFrameError with 819 elements. Creating vector time with 819 elements. Creating vector countGarbledLFrame with 819 elements. Creating vector time with 819 elements. Creating vector cFrameEsecs with 819 elements. Creating vector time with 819 elements. Creating vector correctedSampleCountList with 819 elements. Creating vector time with 819 elements. Creating vector time with 819 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011060/2011.060.01/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011.060.01.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_2011.060.01.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 4 segments. [Warning: MATLAB has disabled some advanced graphics rendering features by switching to software OpenGL. For more information, click here.] Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_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_2011_060_01_060_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_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 = 66 Gridding with nix = 198, iZ = 77 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... bbp420 bbp700 fl700_uncorr N BL BLflow LOPC count transCount nonTransCount LCcount Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB420 cvarname = gB700 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount cvarname = gLOPCtransCount cvarname = gLOPCnonTransCount cvarname = gLOPCLCcount Encountered 0 NaN values in array of lon that is 41856 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: Sampled 41856 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 118877 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 03/01/2011 10:30 to 03/01/2011 15:29 swr = 393.8219 581.9231 549.2627 529.8013 507.9247 365.3228 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_swr.png [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 564) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Done plotting SWR. Executing: /bin/rm -f ../results/2011060_GulperTimes.txt && touch ../results/2011060_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/2011/2011060/2011.060.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2011/2011060/2011.060.01/syslog -startEsecs 1299012573.98 -surveyName Dorado389_2011_060_01_060_01 >> ../results/2011060_GulperTimes.txt Executing: removeGulpDups.py ../results/2011060_GulperTimes.txt Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_gridded.mat outvarstr = 'gF gT gN gS gD gO gB420 gB700 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 gB420 2Column contouring gridded variable gB700 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_2011_060_01_060_01_2column.png Elapsed time to save image: 4 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 gB420 Biolume contouring gridded variable gB700 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_2011_060_01_060_01_biolume.png Elapsed time to save image: 22 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 gB420 2Column contouring gridded variable gB700 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_2011_060_01_060_01_lopc.png Elapsed time to save image: 4 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 128) 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_2011_060_01_060_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_2column.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_biolume.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_lopc.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2011/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_2011_060_01_060_01_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_060_01_060_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_060_01_060_01_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_060_01_060_01_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @420 nm', jetplus, varlimits(5,:), hs2.bbp420, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @700 nm', jetplus, varlimits(6,:), hs2.bbp700, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2011/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.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2011/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_2011_060_01_060_01_Bioluminescence.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2011/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2011_060_01_060_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01.kml... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_060_01_060_01_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_2011_060_01_060_01.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in bbpRed. Interpolating anyway. 1 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 146 NaN values in array of lon that is 6625 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: Sampled 6479 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 6479 are not equal to number of Lat lon points = 6625 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_2011_060_01_060_01.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01.txt... Copied to /mbari/AUVCTD/surveys/2011/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_Gulper.txt... Tried, but failed to copy to /mbari/AUVCTD/surveys/2011/odv/ cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_Gulper.txt’: No such file or directory ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in bbpRed. Interpolating anyway. 1 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_2011_060_01_060_01_decim.nc... Copied to /mbari/AUVCTD/surveys/2011/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_2011_060_01_060_01.nc... Copied to /mbari/AUVCTD/surveys/2011/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01_gridded.mat... Copied to /mbari/AUVCTD/surveys/2011/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_060_01_060_01.mat... Copied to /mbari/AUVCTD/surveys/2011/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2011_060_01_060_01 processed" mccann@mbari.org < mail_Dorado389_2011_060_01_060_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011.060.01.mat Processing time: 112 seconds