Execution of AUVprocess_main version 1.86 at 2018-05-23T22:49:31Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2010, ['340.00';'340.01'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2010.340.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/navigation.nc') Creating vector time with 53140 elements. Creating vector mPos_x with 53140 elements. Creating vector time with 53140 elements. Creating vector mPos_y with 53140 elements. Creating vector time with 53140 elements. Creating vector mDepth with 53140 elements. Creating vector time with 53140 elements. Creating vector mGpsNorth with 53140 elements. Creating vector time with 53140 elements. Creating vector mGpsEast with 53140 elements. Creating vector time with 53140 elements. Creating vector mGpsValid with 53140 elements. Creating vector time with 53140 elements. Creating vector mPhi with 53140 elements. Creating vector time with 53140 elements. Creating vector mTheta with 53140 elements. Creating vector time with 53140 elements. Creating vector mPsi with 53140 elements. Creating vector time with 53140 elements. Creating vector mOmega_x with 53140 elements. Creating vector time with 53140 elements. Creating vector mOmega_y with 53140 elements. Creating vector time with 53140 elements. Creating vector mOmega_z with 53140 elements. Creating vector time with 53140 elements. Creating vector mPsaRange with 53140 elements. Creating vector time with 53140 elements. Creating vector mAltitude with 53140 elements. Creating vector time with 53140 elements. Creating vector mDvlAltitude with 53140 elements. Creating vector time with 53140 elements. Creating vector mWaterSpeed with 53140 elements. Creating vector time with 53140 elements. Creating vector mDvlValid with 53140 elements. Creating vector time with 53140 elements. Creating vector mDvlNewData with 53140 elements. Creating vector time with 53140 elements. Creating vector mDeltaT with 53140 elements. Creating vector time with 53140 elements. Creating vector nfix with 53140 elements. Creating vector time with 53140 elements. Creating vector efix with 53140 elements. Creating vector time with 53140 elements. Creating vector filter_north with 53140 elements. Creating vector time with 53140 elements. Creating vector filter_east with 53140 elements. Creating vector time with 53140 elements. Creating vector filter_depth with 53140 elements. Creating vector time with 53140 elements. Creating vector north_current with 53140 elements. Creating vector time with 53140 elements. Creating vector east_current with 53140 elements. Creating vector time with 53140 elements. Creating vector speed_bias with 53140 elements. Creating vector time with 53140 elements. Creating vector heading_bias with 53140 elements. Creating vector time with 53140 elements. Creating vector latitude with 53140 elements. Creating vector time with 53140 elements. Creating vector longitude with 53140 elements. Creating vector time with 53140 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/navigation.nc'); processNav(): median of positive valued depths = 115.6565 processNav(): Finding depths less than 809.5955 and times > 0 processNav(): length(Nav.depth) = 53140 processNav(): length(gindx) = 53140 Processing GPS navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/gps.nc') Creating vector time with 409 elements. Creating vector hours with 409 elements. Creating vector time with 409 elements. Creating vector minutes with 409 elements. Creating vector time with 409 elements. Creating vector seconds with 409 elements. Creating vector time with 409 elements. Creating vector centiSeconds with 409 elements. Creating vector time with 409 elements. Creating vector latitude with 409 elements. Creating vector time with 409 elements. Creating vector longitude with 409 elements. Creating vector time with 409 elements. Creating vector quality with 409 elements. Creating vector time with 409 elements. Creating vector numberOfSatellites with 409 elements. Creating vector time with 409 elements. Creating vector hdop with 409 elements. Creating vector time with 409 elements. Creating vector antennaHeight with 409 elements. Creating vector time with 409 elements. Creating vector geoHeight with 409 elements. Creating vector time with 409 elements. Creating vector dgpsDataAge with 409 elements. Creating vector time with 409 elements. Creating vector dgpsRSID with 409 elements. Creating vector time with 409 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/parosci.nc') Creating vector time with 97473 elements. Creating vector depth with 97473 elements. Creating vector time with 97473 elements. Creating vector temp with 97473 elements. Creating vector time with 97473 elements. Creating vector pressure with 97473 elements. Creating vector time with 97473 elements. Creating vector temp_period with 97473 elements. Creating vector time with 97473 elements. Creating vector pres_period with 97473 elements. Creating vector time with 97473 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -1.3838 max(Depth.data) = 250.501 Found 2062 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.99834 max(Depth.data) = 250.501 Processing hs2 backscattering and chlorophyll fluorescence data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/hydroscatlog.nc') Creating vector time with 42752 elements. Creating vector Seconds with 42752 elements. Creating vector time with 42752 elements. Creating vector HundrethsOfSeconds with 42752 elements. Creating vector time with 42752 elements. Creating vector Snorm1 with 42752 elements. Creating vector time with 42752 elements. Creating vector Snorm2 with 42752 elements. Creating vector time with 42752 elements. Creating vector Snorm3 with 42752 elements. Creating vector time with 42752 elements. Creating vector Gain_Status_1 with 42752 elements. Creating vector time with 42752 elements. Creating vector Gain_Status_2 with 42752 elements. Creating vector time with 42752 elements. Creating vector Gain_Status_3 with 42752 elements. Creating vector time with 42752 elements. Creating vector RawDepthValue with 42752 elements. Creating vector time with 42752 elements. Creating vector RawTempValue with 42752 elements. Creating vector time with 42752 elements. Creating vector Temperature with 42752 elements. Creating vector time with 42752 elements. Creating vector ErrorValue with 42752 elements. Creating vector time with 42752 elements. Creating vector bb470 with 42752 elements. Creating vector time with 42752 elements. Creating vector bb676 with 42752 elements. Creating vector time with 42752 elements. Creating vector fl676u with 42752 elements. Creating vector time with 42752 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/ctdDriver.nc') Creating vector time with 42597 elements. Creating vector conductivity with 42597 elements. Creating vector time with 42597 elements. Creating vector temperature with 42597 elements. Creating vector time with 42597 elements. Creating vector cond_frequency with 42597 elements. Creating vector time with 42597 elements. Creating vector temp_frequency with 42597 elements. Creating vector time with 42597 elements. Creating vector spare with 42597 elements. Creating vector time with 42597 elements. Creating vector humidity with 42597 elements. Creating vector time with 42597 elements. Creating vector flow1 with 42597 elements. Creating vector time with 42597 elements. Creating vector rhodamine with 42597 elements. Creating vector time with 42597 elements. Creating vector dissolvedO2 with 42597 elements. Creating vector time with 42597 elements. Creating vector salinity with 42597 elements. Creating vector time with 42597 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/ctdDriver2.nc') Creating vector time with 42672 elements. Creating vector conductivity with 42672 elements. Creating vector time with 42672 elements. Creating vector temperature with 42672 elements. Creating vector time with 42672 elements. Creating vector cond_frequency with 42672 elements. Creating vector time with 42672 elements. Creating vector temp_frequency with 42672 elements. Creating vector time with 42672 elements. Creating vector flow2 with 42672 elements. Creating vector time with 42672 elements. Creating vector spare with 42672 elements. Creating vector time with 42672 elements. Creating vector salinity with 42672 elements. Creating vector time with 42672 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/isuslog.nc') Creating vector time with 8272 elements. Creating vector isusNitrate with 8272 elements. Creating vector time with 8272 elements. Creating vector isusTemp with 8272 elements. Creating vector time with 8272 elements. Creating vector isusQuality with 8272 elements. Creating vector time with 8272 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/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/2010/2010340/2010.340.00/biolume.nc') Creating vector time with 10546 elements. Creating vector rrr with 10546 elements. Creating vector time with 10546 elements. Creating vector cal_striing with 10546 elements. Creating vector time with 10546 elements. Creating vector avg_biolume with 10546 elements. Creating vector time with 10546 elements. Creating vector pump with 10546 elements. Creating vector time with 10546 elements. Creating vector system_voltage with 10546 elements. Creating vector time with 10546 elements. Creating vector flow with 10546 elements. Creating vector time with 10546 elements. Creating vector HV with 10546 elements. Creating vector time with 10546 elements. Creating vector reserved with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_0 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_1 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_2 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_3 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_4 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_5 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_6 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_7 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_8 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_9 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_10 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_11 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_12 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_13 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_14 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_15 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_16 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_17 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_18 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_19 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_20 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_21 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_22 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_23 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_24 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_25 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_26 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_27 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_28 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_29 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_30 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_31 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_32 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_33 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_34 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_35 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_36 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_37 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_38 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_39 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_40 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_41 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_42 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_43 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_44 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_45 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_46 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_47 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_48 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_49 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_50 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_51 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_52 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_53 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_54 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_55 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_56 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_57 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_58 with 10546 elements. Creating vector time with 10546 elements. Creating vector raw_59 with 10546 elements. Creating vector time with 10546 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/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/2010/2010340/2010.340.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (1021 x 994) with 1014874 elements. Creating vector time with 1021 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (1021 x 994) with 1014874 elements. Creating vector time with 1021 elements. Creating vector bin with 994 elements. Creating matrix countList (1021 x 994) with 1014874 elements. Creating vector time with 1021 elements. Creating vector bin with 994 elements. Creating vector LCcount with 1021 elements. Creating vector time with 1021 elements. Creating vector transCount with 1021 elements. Creating vector time with 1021 elements. Creating vector nonTransCount with 1021 elements. Creating vector time with 1021 elements. Creating vector ai_mean with 1021 elements. Creating vector time with 1021 elements. Creating vector ai_min with 1021 elements. Creating vector time with 1021 elements. Creating vector ai_max with 1021 elements. Creating vector time with 1021 elements. Creating vector ai_std with 1021 elements. Creating vector time with 1021 elements. Creating vector esd_mean with 1021 elements. Creating vector time with 1021 elements. Creating vector esd_min with 1021 elements. Creating vector time with 1021 elements. Creating vector esd_max with 1021 elements. Creating vector time with 1021 elements. Creating vector esd_std with 1021 elements. Creating vector time with 1021 elements. Creating vector countSum with 1021 elements. Creating vector time with 1021 elements. Creating vector snapshot with 1021 elements. Creating vector time with 1021 elements. Creating vector threshold with 1021 elements. Creating vector time with 1021 elements. Creating vector sampleCount with 1021 elements. Creating vector time with 1021 elements. Creating vector flowCount with 1021 elements. Creating vector time with 1021 elements. Creating vector flowTime with 1021 elements. Creating vector time with 1021 elements. Creating vector bufferStatus with 1021 elements. Creating vector time with 1021 elements. Creating vector laserLevel with 1021 elements. Creating vector time with 1021 elements. Creating vector counter with 1021 elements. Creating vector time with 1021 elements. Creating vector counterPeriod with 1021 elements. Creating vector time with 1021 elements. Creating vector laserControl with 1021 elements. Creating vector time with 1021 elements. Creating vector countUnknownFrameCharacter with 1021 elements. Creating vector time with 1021 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 1021 elements. Creating vector time with 1021 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 1021 elements. Creating vector time with 1021 elements. Creating vector flowSpeed with 1021 elements. Creating vector time with 1021 elements. Creating vector countShortLFrameError with 1021 elements. Creating vector time with 1021 elements. Creating vector countGarbledLFrame with 1021 elements. Creating vector time with 1021 elements. Creating vector cFrameEsecs with 1021 elements. Creating vector time with 1021 elements. Creating vector correctedSampleCountList with 1021 elements. Creating vector time with 1021 elements. Creating vector time with 1021 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.340.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2010.340.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/navigation.nc') Creating vector time with 54069 elements. Creating vector mPos_x with 54069 elements. Creating vector time with 54069 elements. Creating vector mPos_y with 54069 elements. Creating vector time with 54069 elements. Creating vector mDepth with 54069 elements. Creating vector time with 54069 elements. Creating vector mGpsNorth with 54069 elements. Creating vector time with 54069 elements. Creating vector mGpsEast with 54069 elements. Creating vector time with 54069 elements. Creating vector mGpsValid with 54069 elements. Creating vector time with 54069 elements. Creating vector mPhi with 54069 elements. Creating vector time with 54069 elements. Creating vector mTheta with 54069 elements. Creating vector time with 54069 elements. Creating vector mPsi with 54069 elements. Creating vector time with 54069 elements. Creating vector mOmega_x with 54069 elements. Creating vector time with 54069 elements. Creating vector mOmega_y with 54069 elements. Creating vector time with 54069 elements. Creating vector mOmega_z with 54069 elements. Creating vector time with 54069 elements. Creating vector mPsaRange with 54069 elements. Creating vector time with 54069 elements. Creating vector mAltitude with 54069 elements. Creating vector time with 54069 elements. Creating vector mDvlAltitude with 54069 elements. Creating vector time with 54069 elements. Creating vector mWaterSpeed with 54069 elements. Creating vector time with 54069 elements. Creating vector mDvlValid with 54069 elements. Creating vector time with 54069 elements. Creating vector mDvlNewData with 54069 elements. Creating vector time with 54069 elements. Creating vector mDeltaT with 54069 elements. Creating vector time with 54069 elements. Creating vector nfix with 54069 elements. Creating vector time with 54069 elements. Creating vector efix with 54069 elements. Creating vector time with 54069 elements. Creating vector filter_north with 54069 elements. Creating vector time with 54069 elements. Creating vector filter_east with 54069 elements. Creating vector time with 54069 elements. Creating vector filter_depth with 54069 elements. Creating vector time with 54069 elements. Creating vector north_current with 54069 elements. Creating vector time with 54069 elements. Creating vector east_current with 54069 elements. Creating vector time with 54069 elements. Creating vector speed_bias with 54069 elements. Creating vector time with 54069 elements. Creating vector heading_bias with 54069 elements. Creating vector time with 54069 elements. Creating vector latitude with 54069 elements. Creating vector time with 54069 elements. Creating vector longitude with 54069 elements. Creating vector time with 54069 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/navigation.nc'); processNav(): median of positive valued depths = 104.3529 processNav(): Finding depths less than 730.4704 and times > 0 processNav(): length(Nav.depth) = 54069 processNav(): length(gindx) = 54069 Processing GPS navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/gps.nc') Creating vector time with 429 elements. Creating vector hours with 429 elements. Creating vector time with 429 elements. Creating vector minutes with 429 elements. Creating vector time with 429 elements. Creating vector seconds with 429 elements. Creating vector time with 429 elements. Creating vector centiSeconds with 429 elements. Creating vector time with 429 elements. Creating vector latitude with 429 elements. Creating vector time with 429 elements. Creating vector longitude with 429 elements. Creating vector time with 429 elements. Creating vector quality with 429 elements. Creating vector time with 429 elements. Creating vector numberOfSatellites with 429 elements. Creating vector time with 429 elements. Creating vector hdop with 429 elements. Creating vector time with 429 elements. Creating vector antennaHeight with 429 elements. Creating vector time with 429 elements. Creating vector geoHeight with 429 elements. Creating vector time with 429 elements. Creating vector dgpsDataAge with 429 elements. Creating vector time with 429 elements. Creating vector dgpsRSID with 429 elements. Creating vector time with 429 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/parosci.nc') Creating vector time with 99154 elements. Creating vector depth with 99154 elements. Creating vector time with 99154 elements. Creating vector temp with 99154 elements. Creating vector time with 99154 elements. Creating vector pressure with 99154 elements. Creating vector time with 99154 elements. Creating vector temp_period with 99154 elements. Creating vector time with 99154 elements. Creating vector pres_period with 99154 elements. Creating vector time with 99154 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.15194 max(Depth.data) = 250.2904 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.15194 max(Depth.data) = 250.2904 Processing hs2 backscattering and chlorophyll fluorescence data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/hydroscatlog.nc') Creating vector time with 43503 elements. Creating vector Seconds with 43503 elements. Creating vector time with 43503 elements. Creating vector HundrethsOfSeconds with 43503 elements. Creating vector time with 43503 elements. Creating vector Snorm1 with 43503 elements. Creating vector time with 43503 elements. Creating vector Snorm2 with 43503 elements. Creating vector time with 43503 elements. Creating vector Snorm3 with 43503 elements. Creating vector time with 43503 elements. Creating vector Gain_Status_1 with 43503 elements. Creating vector time with 43503 elements. Creating vector Gain_Status_2 with 43503 elements. Creating vector time with 43503 elements. Creating vector Gain_Status_3 with 43503 elements. Creating vector time with 43503 elements. Creating vector RawDepthValue with 43503 elements. Creating vector time with 43503 elements. Creating vector RawTempValue with 43503 elements. Creating vector time with 43503 elements. Creating vector Temperature with 43503 elements. Creating vector time with 43503 elements. Creating vector ErrorValue with 43503 elements. Creating vector time with 43503 elements. Creating vector bb470 with 43503 elements. Creating vector time with 43503 elements. Creating vector bb676 with 43503 elements. Creating vector time with 43503 elements. Creating vector fl676u with 43503 elements. Creating vector time with 43503 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/ctdDriver.nc') Creating vector time with 43417 elements. Creating vector conductivity with 43417 elements. Creating vector time with 43417 elements. Creating vector temperature with 43417 elements. Creating vector time with 43417 elements. Creating vector cond_frequency with 43417 elements. Creating vector time with 43417 elements. Creating vector temp_frequency with 43417 elements. Creating vector time with 43417 elements. Creating vector spare with 43417 elements. Creating vector time with 43417 elements. Creating vector humidity with 43417 elements. Creating vector time with 43417 elements. Creating vector flow1 with 43417 elements. Creating vector time with 43417 elements. Creating vector rhodamine with 43417 elements. Creating vector time with 43417 elements. Creating vector dissolvedO2 with 43417 elements. Creating vector time with 43417 elements. Creating vector salinity with 43417 elements. Creating vector time with 43417 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/ctdDriver2.nc') Creating vector time with 43402 elements. Creating vector conductivity with 43402 elements. Creating vector time with 43402 elements. Creating vector temperature with 43402 elements. Creating vector time with 43402 elements. Creating vector cond_frequency with 43402 elements. Creating vector time with 43402 elements. Creating vector temp_frequency with 43402 elements. Creating vector time with 43402 elements. Creating vector flow2 with 43402 elements. Creating vector time with 43402 elements. Creating vector spare with 43402 elements. Creating vector time with 43402 elements. Creating vector salinity with 43402 elements. Creating vector time with 43402 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/isuslog.nc') Creating vector time with 8429 elements. Creating vector isusNitrate with 8429 elements. Creating vector time with 8429 elements. Creating vector isusTemp with 8429 elements. Creating vector time with 8429 elements. Creating vector isusQuality with 8429 elements. Creating vector time with 8429 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/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/2010/2010340/2010.340.01/biolume.nc') Creating vector time with 10735 elements. Creating vector rrr with 10735 elements. Creating vector time with 10735 elements. Creating vector cal_striing with 10735 elements. Creating vector time with 10735 elements. Creating vector avg_biolume with 10735 elements. Creating vector time with 10735 elements. Creating vector pump with 10735 elements. Creating vector time with 10735 elements. Creating vector system_voltage with 10735 elements. Creating vector time with 10735 elements. Creating vector flow with 10735 elements. Creating vector time with 10735 elements. Creating vector HV with 10735 elements. Creating vector time with 10735 elements. Creating vector reserved with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_0 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_1 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_2 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_3 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_4 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_5 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_6 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_7 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_8 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_9 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_10 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_11 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_12 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_13 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_14 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_15 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_16 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_17 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_18 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_19 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_20 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_21 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_22 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_23 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_24 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_25 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_26 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_27 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_28 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_29 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_30 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_31 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_32 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_33 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_34 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_35 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_36 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_37 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_38 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_39 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_40 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_41 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_42 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_43 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_44 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_45 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_46 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_47 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_48 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_49 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_50 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_51 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_52 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_53 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_54 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_55 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_56 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_57 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_58 with 10735 elements. Creating vector time with 10735 elements. Creating vector raw_59 with 10735 elements. Creating vector time with 10735 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/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/2010/2010340/2010.340.01/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (1037 x 994) with 1030778 elements. Creating vector time with 1037 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (1037 x 994) with 1030778 elements. Creating vector time with 1037 elements. Creating vector bin with 994 elements. Creating matrix countList (1037 x 994) with 1030778 elements. Creating vector time with 1037 elements. Creating vector bin with 994 elements. Creating vector LCcount with 1037 elements. Creating vector time with 1037 elements. Creating vector transCount with 1037 elements. Creating vector time with 1037 elements. Creating vector nonTransCount with 1037 elements. Creating vector time with 1037 elements. Creating vector ai_mean with 1037 elements. Creating vector time with 1037 elements. Creating vector ai_min with 1037 elements. Creating vector time with 1037 elements. Creating vector ai_max with 1037 elements. Creating vector time with 1037 elements. Creating vector ai_std with 1037 elements. Creating vector time with 1037 elements. Creating vector esd_mean with 1037 elements. Creating vector time with 1037 elements. Creating vector esd_min with 1037 elements. Creating vector time with 1037 elements. Creating vector esd_max with 1037 elements. Creating vector time with 1037 elements. Creating vector esd_std with 1037 elements. Creating vector time with 1037 elements. Creating vector countSum with 1037 elements. Creating vector time with 1037 elements. Creating vector snapshot with 1037 elements. Creating vector time with 1037 elements. Creating vector threshold with 1037 elements. Creating vector time with 1037 elements. Creating vector sampleCount with 1037 elements. Creating vector time with 1037 elements. Creating vector flowCount with 1037 elements. Creating vector time with 1037 elements. Creating vector flowTime with 1037 elements. Creating vector time with 1037 elements. Creating vector bufferStatus with 1037 elements. Creating vector time with 1037 elements. Creating vector laserLevel with 1037 elements. Creating vector time with 1037 elements. Creating vector counter with 1037 elements. Creating vector time with 1037 elements. Creating vector counterPeriod with 1037 elements. Creating vector time with 1037 elements. Creating vector laserControl with 1037 elements. Creating vector time with 1037 elements. Creating vector countUnknownFrameCharacter with 1037 elements. Creating vector time with 1037 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 1037 elements. Creating vector time with 1037 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 1037 elements. Creating vector time with 1037 elements. Creating vector flowSpeed with 1037 elements. Creating vector time with 1037 elements. Creating vector countShortLFrameError with 1037 elements. Creating vector time with 1037 elements. Creating vector countGarbledLFrame with 1037 elements. Creating vector time with 1037 elements. Creating vector cFrameEsecs with 1037 elements. Creating vector time with 1037 elements. Creating vector correctedSampleCountList with 1037 elements. Creating vector time with 1037 elements. Creating vector time with 1037 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.340.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Calling build_auv_survey.m to construct survey file... SecondaryDissolvedO2 = [] Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.340.00.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.340.01.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 8 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_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 = 98 Gridding with nix = 294, iZ = 498 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 107018 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 107018 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: 12/06/2010 07:30 to 12/06/2010 15:29 swr = 34.8720 74.2482 207.0908 353.7081 375.5013 340.7449 319.0654 213.4287 126.9169 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2010340_GulperTimes.txt && touch ../results/2010340_GulperTimes.txt Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010340/2010.340.00/syslog -startEsecs 1291666490.0616 -surveyName Dorado389_2010_340_00_340_01 >> ../results/2010340_GulperTimes.txt Executing: removeGulpDups.py ../results/2010340_GulperTimes.txt Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010340/2010.340.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010340/2010.340.01/syslog -startEsecs 1291666490.0616 -surveyName Dorado389_2010_340_00_340_01 >> ../results/2010340_GulperTimes.txt Executing: removeGulpDups.py ../results/2010340_GulperTimes.txt Bottle: 0 Time: 1291656887 Depth: 169.379 Dist: 2.0351 Bottle: 1 Time: 1291658596 Depth: 92.2506 Dist: 4.4926 Bottle: 2 Time: 1291669336 Depth: 146.7764 Dist: 21.1494 Bottle: 3 Time: 1291669990 Depth: 117.2131 Dist: 22.1199 Bottle: 5 Time: 1291674779 Depth: 164.0423 Dist: 28.5303 Bottle: 6 Time: 1291675200 Depth: 54.5123 Dist: 28.9867 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_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 Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gS Drawing bottom contour from EM300 data 2Column contouring gridded variable gN Drawing bottom contour from EM300 data 2Column contouring gridded variable gO Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_2column.png Elapsed time to save image: 10 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN Drawing bottom contour from EM300 data Biolume contouring gridded variable gO Drawing bottom contour from EM300 data Biolume contouring gridded variable gB420 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB700 Drawing bottom contour from EM300 data Biolume contouring gridded variable gF Drawing bottom contour from EM300 data Biolume contouring gridded variable gBL Drawing bottom contour from EM300 data Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_biolume.png Elapsed time to save image: 40 seconds 2Column contouring gridded variable gLOPCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCtransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCnonTransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCLCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_lopc.png Elapsed time to save image: 12 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_2010_340_00_340_01_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_2column.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_biolume.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_lopc.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing KML files ... KML = write_kml(survey_shrt_filename_base, 'Temperature', jetplus, varlimits(1,:), ctd1.T, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Nitrate.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @420 nm', jetplus, varlimits(5,:), hs2.bbp420, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Optical_Backscatter_420_nm.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @700 nm', jetplus, varlimits(6,:), hs2.bbp700, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Chlorophyll_Fluorescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_LOPC_Total_Count.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_01_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2010_340_00_340_01.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01.kml... Copied to /mbari/AUVCTD/surveys/2010/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2010_340_00_340_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_2010_340_00_340_01.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 4 NaNs found in bbpRed. Interpolating anyway. Encountered 31 NaN values in array of lon that is 16690 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 16659 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 16659 are not equal to number of Lat lon points = 16690 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_2010_340_00_340_01.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01.txt... Copied to /mbari/AUVCTD/surveys/2010/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2010/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 4 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_decim.nc... Copied to /mbari/AUVCTD/surveys/2010/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01.nc... Copied to /mbari/AUVCTD/surveys/2010/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01_gridded.mat... Copied to /mbari/AUVCTD/surveys/2010/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_340_00_340_01.mat... Copied to /mbari/AUVCTD/surveys/2010/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2010_340_00_340_01 processed" mccann@mbari.org < mail_Dorado389_2010_340_00_340_01.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.340.00.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.340.01.mat Processing time: 151 seconds