Execution of AUVprocess_main version 1.86 at 2018-05-24T16:59:38Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2013, ['076.01';'076.02'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2013.076.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/ 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/2013/2013076/2013.076.01/navigation.nc') Creating vector time with 14514 elements. Creating vector mPos_x with 14514 elements. Creating vector time with 14514 elements. Creating vector mPos_y with 14514 elements. Creating vector time with 14514 elements. Creating vector mDepth with 14514 elements. Creating vector time with 14514 elements. Creating vector mGpsNorth with 14514 elements. Creating vector time with 14514 elements. Creating vector mGpsEast with 14514 elements. Creating vector time with 14514 elements. Creating vector mGpsValid with 14514 elements. Creating vector time with 14514 elements. Creating vector mPhi with 14514 elements. Creating vector time with 14514 elements. Creating vector mTheta with 14514 elements. Creating vector time with 14514 elements. Creating vector mPsi with 14514 elements. Creating vector time with 14514 elements. Creating vector mOmega_x with 14514 elements. Creating vector time with 14514 elements. Creating vector mOmega_y with 14514 elements. Creating vector time with 14514 elements. Creating vector mOmega_z with 14514 elements. Creating vector time with 14514 elements. Creating vector mPsaRange with 14514 elements. Creating vector time with 14514 elements. Creating vector mAltitude with 14514 elements. Creating vector time with 14514 elements. Creating vector mDvlAltitude with 14514 elements. Creating vector time with 14514 elements. Creating vector mEchoAltitude with 14514 elements. Creating vector time with 14514 elements. Creating vector mEchoHorizRange with 14514 elements. Creating vector time with 14514 elements. Creating vector mEchoAltitudeLast with 14514 elements. Creating vector time with 14514 elements. Creating vector mEchoHorizRangeLast with 14514 elements. Creating vector time with 14514 elements. Creating vector mEchoNumOfPings with 14514 elements. Creating vector time with 14514 elements. Creating vector mWaterSpeed with 14514 elements. Creating vector time with 14514 elements. Creating vector mDvlValid with 14514 elements. Creating vector time with 14514 elements. Creating vector mDvlNewData with 14514 elements. Creating vector time with 14514 elements. Creating vector mDeltaT with 14514 elements. Creating vector time with 14514 elements. Creating vector nfix with 14514 elements. Creating vector time with 14514 elements. Creating vector efix with 14514 elements. Creating vector time with 14514 elements. Creating vector filter_north with 14514 elements. Creating vector time with 14514 elements. Creating vector filter_east with 14514 elements. Creating vector time with 14514 elements. Creating vector filter_depth with 14514 elements. Creating vector time with 14514 elements. Creating vector north_current with 14514 elements. Creating vector time with 14514 elements. Creating vector east_current with 14514 elements. Creating vector time with 14514 elements. Creating vector speed_bias with 14514 elements. Creating vector time with 14514 elements. Creating vector heading_bias with 14514 elements. Creating vector time with 14514 elements. Creating vector latitude with 14514 elements. Creating vector time with 14514 elements. Creating vector longitude with 14514 elements. Creating vector time with 14514 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/navigation.nc'); processNav(): median of positive valued depths = 35.3422 processNav(): Finding depths less than 247.3954 and times > 0 processNav(): length(Nav.depth) = 14514 processNav(): length(gindx) = 14514 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/2013/2013076/2013.076.01/gps.nc') Creating vector time with 485 elements. Creating vector hours with 485 elements. Creating vector time with 485 elements. Creating vector minutes with 485 elements. Creating vector time with 485 elements. Creating vector seconds with 485 elements. Creating vector time with 485 elements. Creating vector centiSeconds with 485 elements. Creating vector time with 485 elements. Creating vector latitude with 485 elements. Creating vector time with 485 elements. Creating vector longitude with 485 elements. Creating vector time with 485 elements. Creating vector quality with 485 elements. Creating vector time with 485 elements. Creating vector numberOfSatellites with 485 elements. Creating vector time with 485 elements. Creating vector hdop with 485 elements. Creating vector time with 485 elements. Creating vector antennaHeight with 485 elements. Creating vector time with 485 elements. Creating vector geoHeight with 485 elements. Creating vector time with 485 elements. Creating vector dgpsDataAge with 485 elements. Creating vector time with 485 elements. Creating vector dgpsRSID with 485 elements. Creating vector time with 485 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/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/2013/2013076/2013.076.01/parosci.nc') Creating vector time with 24372 elements. Creating vector depth with 24372 elements. Creating vector time with 24372 elements. Creating vector temp with 24372 elements. Creating vector time with 24372 elements. Creating vector pressure with 24372 elements. Creating vector time with 24372 elements. Creating vector temp_period with 24372 elements. Creating vector time with 24372 elements. Creating vector pres_period with 24372 elements. Creating vector time with 24372 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.18742 max(Depth.data) = 80.7489 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.18742 max(Depth.data) = 80.7489 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/2013/2013076/2013.076.01/hydroscatlog.nc') Creating vector time with 11737 elements. Creating vector Seconds with 11737 elements. Creating vector time with 11737 elements. Creating vector HundrethsOfSeconds with 11737 elements. Creating vector time with 11737 elements. Creating vector Snorm1 with 11737 elements. Creating vector time with 11737 elements. Creating vector Snorm2 with 11737 elements. Creating vector time with 11737 elements. Creating vector Snorm3 with 11737 elements. Creating vector time with 11737 elements. Creating vector Gain_Status_1 with 11737 elements. Creating vector time with 11737 elements. Creating vector Gain_Status_2 with 11737 elements. Creating vector time with 11737 elements. Creating vector Gain_Status_3 with 11737 elements. Creating vector time with 11737 elements. Creating vector RawDepthValue with 11737 elements. Creating vector time with 11737 elements. Creating vector RawTempValue with 11737 elements. Creating vector time with 11737 elements. Creating vector Temperature with 11737 elements. Creating vector time with 11737 elements. Creating vector ErrorValue with 11737 elements. Creating vector time with 11737 elements. Creating vector bb470 with 11737 elements. Creating vector time with 11737 elements. Creating vector bb676 with 11737 elements. Creating vector time with 11737 elements. Creating vector fl676u with 11737 elements. Creating vector time with 11737 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/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/2013/2013076/2013.076.01/ctdDriver.nc') Creating vector time with 11690 elements. Creating vector conductivity with 11690 elements. Creating vector time with 11690 elements. Creating vector temperature with 11690 elements. Creating vector time with 11690 elements. Creating vector cond_frequency with 11690 elements. Creating vector time with 11690 elements. Creating vector temp_frequency with 11690 elements. Creating vector time with 11690 elements. Creating vector spare with 11690 elements. Creating vector time with 11690 elements. Creating vector humidity with 11690 elements. Creating vector time with 11690 elements. Creating vector flow1 with 11690 elements. Creating vector time with 11690 elements. Creating vector CDOM with 11690 elements. Creating vector time with 11690 elements. Creating vector dissolvedO2 with 11690 elements. Creating vector time with 11690 elements. Creating vector salinity with 11690 elements. Creating vector time with 11690 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/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/2013/2013076/2013.076.01/ctdDriver2.nc') Creating vector time with 11689 elements. Creating vector conductivity with 11689 elements. Creating vector time with 11689 elements. Creating vector temperature with 11689 elements. Creating vector time with 11689 elements. Creating vector cond_frequency with 11689 elements. Creating vector time with 11689 elements. Creating vector temp_frequency with 11689 elements. Creating vector time with 11689 elements. Creating vector flow2 with 11689 elements. Creating vector time with 11689 elements. Creating vector spare with 11689 elements. Creating vector time with 11689 elements. Creating vector salinity with 11689 elements. Creating vector time with 11689 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/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/2013/2013076/2013.076.01/isuslog.nc') Creating vector time with 2668 elements. Creating vector isusNitrate with 2668 elements. Creating vector time with 2668 elements. Creating vector isusTemp with 2668 elements. Creating vector time with 2668 elements. Creating vector isusQuality with 2668 elements. Creating vector time with 2668 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/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/2013/2013076/2013.076.01/biolume.nc') Creating vector time with 2892 elements. Creating vector rrr with 2892 elements. Creating vector time with 2892 elements. Creating vector cal_striing with 2892 elements. Creating vector time with 2892 elements. Creating vector avg_biolume with 2892 elements. Creating vector time with 2892 elements. Creating vector pump with 2892 elements. Creating vector time with 2892 elements. Creating vector system_voltage with 2892 elements. Creating vector time with 2892 elements. Creating vector flow with 2892 elements. Creating vector time with 2892 elements. Creating vector HV with 2892 elements. Creating vector time with 2892 elements. Creating vector reserved with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_0 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_1 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_2 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_3 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_4 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_5 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_6 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_7 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_8 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_9 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_10 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_11 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_12 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_13 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_14 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_15 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_16 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_17 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_18 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_19 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_20 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_21 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_22 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_23 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_24 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_25 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_26 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_27 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_28 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_29 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_30 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_31 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_32 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_33 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_34 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_35 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_36 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_37 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_38 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_39 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_40 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_41 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_42 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_43 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_44 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_45 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_46 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_47 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_48 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_49 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_50 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_51 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_52 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_53 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_54 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_55 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_56 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_57 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_58 with 2892 elements. Creating vector time with 2892 elements. Creating vector raw_59 with 2892 elements. Creating vector time with 2892 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/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/2013/2013076/2013.076.01/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (264 x 994) with 262416 elements. Creating vector time with 264 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (264 x 994) with 262416 elements. Creating vector time with 264 elements. Creating vector bin with 994 elements. Creating matrix countList (264 x 994) with 262416 elements. Creating vector time with 264 elements. Creating vector bin with 994 elements. Creating vector LCcount with 264 elements. Creating vector time with 264 elements. Creating vector transCount with 264 elements. Creating vector time with 264 elements. Creating vector nonTransCount with 264 elements. Creating vector time with 264 elements. Creating vector ai_mean with 264 elements. Creating vector time with 264 elements. Creating vector ai_min with 264 elements. Creating vector time with 264 elements. Creating vector ai_max with 264 elements. Creating vector time with 264 elements. Creating vector ai_std with 264 elements. Creating vector time with 264 elements. Creating vector esd_mean with 264 elements. Creating vector time with 264 elements. Creating vector esd_min with 264 elements. Creating vector time with 264 elements. Creating vector esd_max with 264 elements. Creating vector time with 264 elements. Creating vector esd_std with 264 elements. Creating vector time with 264 elements. Creating vector countSum with 264 elements. Creating vector time with 264 elements. Creating vector snapshot with 264 elements. Creating vector time with 264 elements. Creating vector threshold with 264 elements. Creating vector time with 264 elements. Creating vector sampleCount with 264 elements. Creating vector time with 264 elements. Creating vector flowCount with 264 elements. Creating vector time with 264 elements. Creating vector flowTime with 264 elements. Creating vector time with 264 elements. Creating vector bufferStatus with 264 elements. Creating vector time with 264 elements. Creating vector laserLevel with 264 elements. Creating vector time with 264 elements. Creating vector counter with 264 elements. Creating vector time with 264 elements. Creating vector counterPeriod with 264 elements. Creating vector time with 264 elements. Creating vector laserControl with 264 elements. Creating vector time with 264 elements. Creating vector countUnknownFrameCharacter with 264 elements. Creating vector time with 264 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 264 elements. Creating vector time with 264 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 264 elements. Creating vector time with 264 elements. Creating vector flowSpeed with 264 elements. Creating vector time with 264 elements. Creating vector countShortLFrameError with 264 elements. Creating vector time with 264 elements. Creating vector countGarbledLFrame with 264 elements. Creating vector time with 264 elements. Creating vector cFrameEsecs with 264 elements. Creating vector time with 264 elements. Creating vector correctedSampleCountList with 264 elements. Creating vector time with 264 elements. Creating vector time with 264 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.01/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.076.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2013.076.02 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/navigation.nc') Creating vector time with 52864 elements. Creating vector mPos_x with 52864 elements. Creating vector time with 52864 elements. Creating vector mPos_y with 52864 elements. Creating vector time with 52864 elements. Creating vector mDepth with 52864 elements. Creating vector time with 52864 elements. Creating vector mGpsNorth with 52864 elements. Creating vector time with 52864 elements. Creating vector mGpsEast with 52864 elements. Creating vector time with 52864 elements. Creating vector mGpsValid with 52864 elements. Creating vector time with 52864 elements. Creating vector mPhi with 52864 elements. Creating vector time with 52864 elements. Creating vector mTheta with 52864 elements. Creating vector time with 52864 elements. Creating vector mPsi with 52864 elements. Creating vector time with 52864 elements. Creating vector mOmega_x with 52864 elements. Creating vector time with 52864 elements. Creating vector mOmega_y with 52864 elements. Creating vector time with 52864 elements. Creating vector mOmega_z with 52864 elements. Creating vector time with 52864 elements. Creating vector mPsaRange with 52864 elements. Creating vector time with 52864 elements. Creating vector mAltitude with 52864 elements. Creating vector time with 52864 elements. Creating vector mDvlAltitude with 52864 elements. Creating vector time with 52864 elements. Creating vector mEchoAltitude with 52864 elements. Creating vector time with 52864 elements. Creating vector mEchoHorizRange with 52864 elements. Creating vector time with 52864 elements. Creating vector mEchoAltitudeLast with 52864 elements. Creating vector time with 52864 elements. Creating vector mEchoHorizRangeLast with 52864 elements. Creating vector time with 52864 elements. Creating vector mEchoNumOfPings with 52864 elements. Creating vector time with 52864 elements. Creating vector mWaterSpeed with 52864 elements. Creating vector time with 52864 elements. Creating vector mDvlValid with 52864 elements. Creating vector time with 52864 elements. Creating vector mDvlNewData with 52864 elements. Creating vector time with 52864 elements. Creating vector mDeltaT with 52864 elements. Creating vector time with 52864 elements. Creating vector nfix with 52864 elements. Creating vector time with 52864 elements. Creating vector efix with 52864 elements. Creating vector time with 52864 elements. Creating vector filter_north with 52864 elements. Creating vector time with 52864 elements. Creating vector filter_east with 52864 elements. Creating vector time with 52864 elements. Creating vector filter_depth with 52864 elements. Creating vector time with 52864 elements. Creating vector north_current with 52864 elements. Creating vector time with 52864 elements. Creating vector east_current with 52864 elements. Creating vector time with 52864 elements. Creating vector speed_bias with 52864 elements. Creating vector time with 52864 elements. Creating vector heading_bias with 52864 elements. Creating vector time with 52864 elements. Creating vector latitude with 52864 elements. Creating vector time with 52864 elements. Creating vector longitude with 52864 elements. Creating vector time with 52864 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/navigation.nc'); processNav(): median of positive valued depths = 21.6038 processNav(): Finding depths less than 151.2263 and times > 0 processNav(): length(Nav.depth) = 52864 processNav(): length(gindx) = 52864 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/2013/2013076/2013.076.02/gps.nc') Creating vector time with 2428 elements. Creating vector hours with 2428 elements. Creating vector time with 2428 elements. Creating vector minutes with 2428 elements. Creating vector time with 2428 elements. Creating vector seconds with 2428 elements. Creating vector time with 2428 elements. Creating vector centiSeconds with 2428 elements. Creating vector time with 2428 elements. Creating vector latitude with 2428 elements. Creating vector time with 2428 elements. Creating vector longitude with 2428 elements. Creating vector time with 2428 elements. Creating vector quality with 2428 elements. Creating vector time with 2428 elements. Creating vector numberOfSatellites with 2428 elements. Creating vector time with 2428 elements. Creating vector hdop with 2428 elements. Creating vector time with 2428 elements. Creating vector antennaHeight with 2428 elements. Creating vector time with 2428 elements. Creating vector geoHeight with 2428 elements. Creating vector time with 2428 elements. Creating vector dgpsDataAge with 2428 elements. Creating vector time with 2428 elements. Creating vector dgpsRSID with 2428 elements. Creating vector time with 2428 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/parosci.nc') Creating vector time with 89879 elements. Creating vector depth with 89879 elements. Creating vector time with 89879 elements. Creating vector temp with 89879 elements. Creating vector time with 89879 elements. Creating vector pressure with 89879 elements. Creating vector time with 89879 elements. Creating vector temp_period with 89879 elements. Creating vector time with 89879 elements. Creating vector pres_period with 89879 elements. Creating vector time with 89879 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.1816 max(Depth.data) = 80.7922 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.1816 max(Depth.data) = 80.7922 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/2013/2013076/2013.076.02/hydroscatlog.nc') Creating vector time with 42400 elements. Creating vector Seconds with 42400 elements. Creating vector time with 42400 elements. Creating vector HundrethsOfSeconds with 42400 elements. Creating vector time with 42400 elements. Creating vector Snorm1 with 42400 elements. Creating vector time with 42400 elements. Creating vector Snorm2 with 42400 elements. Creating vector time with 42400 elements. Creating vector Snorm3 with 42400 elements. Creating vector time with 42400 elements. Creating vector Gain_Status_1 with 42400 elements. Creating vector time with 42400 elements. Creating vector Gain_Status_2 with 42400 elements. Creating vector time with 42400 elements. Creating vector Gain_Status_3 with 42400 elements. Creating vector time with 42400 elements. Creating vector RawDepthValue with 42400 elements. Creating vector time with 42400 elements. Creating vector RawTempValue with 42400 elements. Creating vector time with 42400 elements. Creating vector Temperature with 42400 elements. Creating vector time with 42400 elements. Creating vector ErrorValue with 42400 elements. Creating vector time with 42400 elements. Creating vector bb470 with 42400 elements. Creating vector time with 42400 elements. Creating vector bb676 with 42400 elements. Creating vector time with 42400 elements. Creating vector fl676u with 42400 elements. Creating vector time with 42400 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/ctdDriver.nc') Creating vector time with 42331 elements. Creating vector conductivity with 42331 elements. Creating vector time with 42331 elements. Creating vector temperature with 42331 elements. Creating vector time with 42331 elements. Creating vector cond_frequency with 42331 elements. Creating vector time with 42331 elements. Creating vector temp_frequency with 42331 elements. Creating vector time with 42331 elements. Creating vector spare with 42331 elements. Creating vector time with 42331 elements. Creating vector humidity with 42331 elements. Creating vector time with 42331 elements. Creating vector flow1 with 42331 elements. Creating vector time with 42331 elements. Creating vector CDOM with 42331 elements. Creating vector time with 42331 elements. Creating vector dissolvedO2 with 42331 elements. Creating vector time with 42331 elements. Creating vector salinity with 42331 elements. Creating vector time with 42331 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/ctdDriver2.nc') Creating vector time with 42330 elements. Creating vector conductivity with 42330 elements. Creating vector time with 42330 elements. Creating vector temperature with 42330 elements. Creating vector time with 42330 elements. Creating vector cond_frequency with 42330 elements. Creating vector time with 42330 elements. Creating vector temp_frequency with 42330 elements. Creating vector time with 42330 elements. Creating vector flow2 with 42330 elements. Creating vector time with 42330 elements. Creating vector spare with 42330 elements. Creating vector time with 42330 elements. Creating vector salinity with 42330 elements. Creating vector time with 42330 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/isuslog.nc') Creating vector time with 9800 elements. Creating vector isusNitrate with 9800 elements. Creating vector time with 9800 elements. Creating vector isusTemp with 9800 elements. Creating vector time with 9800 elements. Creating vector isusQuality with 9800 elements. Creating vector time with 9800 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/biolume.nc') Creating vector time with 10433 elements. Creating vector rrr with 10433 elements. Creating vector time with 10433 elements. Creating vector cal_striing with 10433 elements. Creating vector time with 10433 elements. Creating vector avg_biolume with 10433 elements. Creating vector time with 10433 elements. Creating vector pump with 10433 elements. Creating vector time with 10433 elements. Creating vector system_voltage with 10433 elements. Creating vector time with 10433 elements. Creating vector flow with 10433 elements. Creating vector time with 10433 elements. Creating vector HV with 10433 elements. Creating vector time with 10433 elements. Creating vector reserved with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_0 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_1 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_2 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_3 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_4 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_5 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_6 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_7 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_8 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_9 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_10 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_11 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_12 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_13 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_14 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_15 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_16 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_17 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_18 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_19 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_20 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_21 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_22 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_23 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_24 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_25 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_26 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_27 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_28 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_29 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_30 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_31 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_32 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_33 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_34 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_35 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_36 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_37 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_38 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_39 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_40 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_41 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_42 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_43 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_44 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_45 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_46 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_47 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_48 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_49 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_50 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_51 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_52 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_53 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_54 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_55 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_56 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_57 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_58 with 10433 elements. Creating vector time with 10433 elements. Creating vector raw_59 with 10433 elements. Creating vector time with 10433 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/biolume.nc'); Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (613 x 994) with 609322 elements. Creating vector time with 613 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (613 x 994) with 609322 elements. Creating vector time with 613 elements. Creating vector bin with 994 elements. Creating matrix countList (613 x 994) with 609322 elements. Creating vector time with 613 elements. Creating vector bin with 994 elements. Creating vector LCcount with 613 elements. Creating vector time with 613 elements. Creating vector transCount with 613 elements. Creating vector time with 613 elements. Creating vector nonTransCount with 613 elements. Creating vector time with 613 elements. Creating vector ai_mean with 613 elements. Creating vector time with 613 elements. Creating vector ai_min with 613 elements. Creating vector time with 613 elements. Creating vector ai_max with 613 elements. Creating vector time with 613 elements. Creating vector ai_std with 613 elements. Creating vector time with 613 elements. Creating vector esd_mean with 613 elements. Creating vector time with 613 elements. Creating vector esd_min with 613 elements. Creating vector time with 613 elements. Creating vector esd_max with 613 elements. Creating vector time with 613 elements. Creating vector esd_std with 613 elements. Creating vector time with 613 elements. Creating vector countSum with 613 elements. Creating vector time with 613 elements. Creating vector snapshot with 613 elements. Creating vector time with 613 elements. Creating vector threshold with 613 elements. Creating vector time with 613 elements. Creating vector sampleCount with 613 elements. Creating vector time with 613 elements. Creating vector flowCount with 613 elements. Creating vector time with 613 elements. Creating vector flowTime with 613 elements. Creating vector time with 613 elements. Creating vector bufferStatus with 613 elements. Creating vector time with 613 elements. Creating vector laserLevel with 613 elements. Creating vector time with 613 elements. Creating vector counter with 613 elements. Creating vector time with 613 elements. Creating vector counterPeriod with 613 elements. Creating vector time with 613 elements. Creating vector laserControl with 613 elements. Creating vector time with 613 elements. Creating vector countUnknownFrameCharacter with 613 elements. Creating vector time with 613 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 613 elements. Creating vector time with 613 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 613 elements. Creating vector time with 613 elements. Creating vector flowSpeed with 613 elements. Creating vector time with 613 elements. Creating vector countShortLFrameError with 613 elements. Creating vector time with 613 elements. Creating vector countGarbledLFrame with 613 elements. Creating vector time with 613 elements. Creating vector cFrameEsecs with 613 elements. Creating vector time with 613 elements. Creating vector correctedSampleCountList with 613 elements. Creating vector time with 613 elements. Creating vector time with 613 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2013/2013076/2013.076.02/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.076.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Calling build_auv_survey.m to construct survey file... SecondaryDissolvedO2 = [] Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.076.01.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.076.02.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 10 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02.mat ************************************************************************* Calling plot_sections from ../viz to produce section plots ... Using median boxcar filter of vector... Using mean boxcar filter of vector... Number of profiles found = 86 Gridding with nix = 258, iZ = 158 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 57599 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. Getting short wave radiation data from M1 for little plot above the biolume section plot Creating vector TIME with 118894 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 03/17/2013 06:30 to 03/17/2013 12:30 swr = NaN 46.4438 225.7151 349.4489 554.6074 633.5027 808.4438 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_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/2013076_GulperTimes.txt && touch ../results/2013076_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/2013/2013076/2013.076.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013076/2013.076.01/syslog -startEsecs 1363538270.5236 -surveyName Dorado389_2013_076_01_076_02 >> ../results/2013076_GulperTimes.txt Executing: removeGulpDups.py ../results/2013076_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/2013/2013076/2013.076.02/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2013/2013076/2013.076.02/syslog -startEsecs 1363538270.5236 -surveyName Dorado389_2013_076_01_076_02 >> ../results/2013076_GulperTimes.txt Executing: removeGulpDups.py ../results/2013076_GulperTimes.txt Bottle: 0 Time: 1363535929 Depth: 12.4198 Dist: 1.1992 Bottle: 1 Time: 1363539192 Depth: 6.7659 Dist: 5.3233 Bottle: 2 Time: 1363540442 Depth: 6.3174 Dist: 7.1904 Bottle: 3 Time: 1363541678 Depth: 7.0314 Dist: 8.9861 Bottle: 4 Time: 1363543767 Depth: 3.843 Dist: 11.9078 Bottle: 5 Time: 1363543827 Depth: 30.6236 Dist: 11.9832 Bottle: 6 Time: 1363546684 Depth: 7.2477 Dist: 15.8324 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_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_2013_076_01_076_02_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 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_2013_076_01_076_02_biolume.png Elapsed time to save image: 25 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_2013_076_01_076_02_lopc.png Elapsed time to save image: 5 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_2013_076_01_076_02_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_2column.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_biolume.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_lopc.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2013/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2013/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_2013_076_01_076_02_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_076_01_076_02_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_076_01_076_02_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_076_01_076_02_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_076_01_076_02_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_076_01_076_02_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_076_01_076_02_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_076_01_076_02_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_076_01_076_02_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_076_01_076_02_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_076_01_076_02_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_076_01_076_02_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_076_01_076_02_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_076_01_076_02_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_076_01_076_02_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_076_01_076_02_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2013/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_2013_076_01_076_02_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_076_01_076_02_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2013_076_01_076_02.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02.kml... Copied to /mbari/AUVCTD/surveys/2013/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2013_076_01_076_02_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 414) In build_auv_survey (line 522) In AUVprocess_main (line 255)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 5 NaNs found in bbpRed. Interpolating anyway. Encountered 1791 NaN values in array of lon that is 12260 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_2013_076_01_076_02.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02.txt... Copied to /mbari/AUVCTD/surveys/2013/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2013/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 5 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_decim.nc... Copied to /mbari/AUVCTD/surveys/2013/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_2013_076_01_076_02.nc... Copied to /mbari/AUVCTD/surveys/2013/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02_gridded.mat... Copied to /mbari/AUVCTD/surveys/2013/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013_076_01_076_02.mat... Copied to /mbari/AUVCTD/surveys/2013/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2013_076_01_076_02 processed" mccann@mbari.org < mail_Dorado389_2013_076_01_076_02.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.076.01.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2013.076.02.mat Processing time: 105 seconds