Execution of AUVprocess_main version 1.86 at 2018-06-02T03:56:57Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2003, ['309.00';'309.01';'309.02';'309.04'], '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: 2003.309.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/ 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/2003/2003309/2003.309.00/navigation.nc') Creating vector time with 101150 elements. Creating vector mPos_x with 101150 elements. Creating vector time with 101150 elements. Creating vector mPos_y with 101150 elements. Creating vector time with 101150 elements. Creating vector mDepth with 101150 elements. Creating vector time with 101150 elements. Creating vector mGpsNorth with 101150 elements. Creating vector time with 101150 elements. Creating vector mGpsEast with 101150 elements. Creating vector time with 101150 elements. Creating vector mGpsValid with 101150 elements. Creating vector time with 101150 elements. Creating vector mPhi with 101150 elements. Creating vector time with 101150 elements. Creating vector mTheta with 101150 elements. Creating vector time with 101150 elements. Creating vector mPsi with 101150 elements. Creating vector time with 101150 elements. Creating vector mOmega_x with 101150 elements. Creating vector time with 101150 elements. Creating vector mOmega_y with 101150 elements. Creating vector time with 101150 elements. Creating vector mOmega_z with 101150 elements. Creating vector time with 101150 elements. Creating vector mPsaRange with 101150 elements. Creating vector time with 101150 elements. Creating vector mAltitude with 101150 elements. Creating vector time with 101150 elements. Creating vector mWaterSpeed with 101150 elements. Creating vector time with 101150 elements. Creating vector nfix with 101150 elements. Creating vector time with 101150 elements. Creating vector efix with 101150 elements. Creating vector time with 101150 elements. Creating vector filter_north with 101150 elements. Creating vector time with 101150 elements. Creating vector filter_east with 101150 elements. Creating vector time with 101150 elements. Creating vector filter_depth with 101150 elements. Creating vector time with 101150 elements. Creating vector north_current with 101150 elements. Creating vector time with 101150 elements. Creating vector east_current with 101150 elements. Creating vector time with 101150 elements. Creating vector speed_bias with 101150 elements. Creating vector time with 101150 elements. Creating vector heading_bias with 101150 elements. Creating vector time with 101150 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/navigation.nc'); processNav(): median of positive valued depths = 114.2906 processNav(): Finding depths less than 800.0345 and times > 0 processNav(): length(Nav.depth) = 101150 processNav(): length(gindx) = 101150 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/2003/2003309/2003.309.00/gps.nc') Creating vector time with 1106 elements. Creating vector UTCTime with 1106 elements. Creating vector time with 1106 elements. Creating vector latitude with 1106 elements. Creating vector time with 1106 elements. Creating vector longitude with 1106 elements. Creating vector time with 1106 elements. Creating vector quality with 1106 elements. Creating vector time with 1106 elements. Creating vector numberOfSatellites with 1106 elements. Creating vector time with 1106 elements. Creating vector hdop with 1106 elements. Creating vector time with 1106 elements. Creating vector antennaHeight with 1106 elements. Creating vector time with 1106 elements. Creating vector geoHeight with 1106 elements. Creating vector time with 1106 elements. Creating vector dgpsDataAge with 1106 elements. Creating vector time with 1106 elements. Creating vector dgpsRSID with 1106 elements. Creating vector time with 1106 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/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/2003/2003309/2003.309.00/parosci.nc') Creating vector time with 101252 elements. Creating vector depth with 101252 elements. Creating vector time with 101252 elements. Creating vector temp with 101252 elements. Creating vector time with 101252 elements. Creating vector pressure with 101252 elements. Creating vector time with 101252 elements. Creating vector temp_period with 101252 elements. Creating vector time with 101252 elements. Creating vector pres_period with 101252 elements. Creating vector time with 101252 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.18727 max(Depth.data) = 250.8653 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.18727 max(Depth.data) = 250.8653 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/2003/2003309/2003.309.00/hydroscatlog.nc') Creating vector time with 80952 elements. Creating vector Seconds with 80952 elements. Creating vector time with 80952 elements. Creating vector HundrethsOfSeconds with 80952 elements. Creating vector time with 80952 elements. Creating vector Snorm1 with 80952 elements. Creating vector time with 80952 elements. Creating vector Snorm2 with 80952 elements. Creating vector time with 80952 elements. Creating vector Snorm3 with 80952 elements. Creating vector time with 80952 elements. Creating vector Gain_Status_1 with 80952 elements. Creating vector time with 80952 elements. Creating vector Gain_Status_2 with 80952 elements. Creating vector time with 80952 elements. Creating vector Gain_Status_3 with 80952 elements. Creating vector time with 80952 elements. Creating vector RawDepthValue with 80952 elements. Creating vector time with 80952 elements. Creating vector RawTempValue with 80952 elements. Creating vector time with 80952 elements. Creating vector Temperature with 80952 elements. Creating vector time with 80952 elements. Creating vector ErrorValue with 80952 elements. Creating vector time with 80952 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/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/2003/2003309/2003.309.00/ctdDriver.nc') Creating vector time with 80927 elements. Creating vector conductivity with 80927 elements. Creating vector time with 80927 elements. Creating vector temperature with 80927 elements. Creating vector time with 80927 elements. Creating vector cond_frequency with 80927 elements. Creating vector time with 80927 elements. Creating vector temp_frequency with 80927 elements. Creating vector time with 80927 elements. Creating vector spare with 80927 elements. Creating vector time with 80927 elements. Creating vector humidity with 80927 elements. Creating vector time with 80927 elements. Creating vector flow1 with 80927 elements. Creating vector time with 80927 elements. Creating vector OBS with 80927 elements. Creating vector time with 80927 elements. Creating vector dissolvedO2 with 80927 elements. Creating vector time with 80927 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/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/2003/2003309/2003.309.00/ctdDriver2.nc') Creating vector time with 80928 elements. Creating vector conductivity with 80928 elements. Creating vector time with 80928 elements. Creating vector temperature with 80928 elements. Creating vector time with 80928 elements. Creating vector cond_frequency with 80928 elements. Creating vector time with 80928 elements. Creating vector temp_frequency with 80928 elements. Creating vector time with 80928 elements. Creating vector flow2 with 80928 elements. Creating vector time with 80928 elements. Creating vector spare with 80928 elements. Creating vector time with 80928 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/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/2003/2003309/2003.309.00/isuslog.nc') Creating vector time with 12222 elements. Creating vector isusNitrate with 12222 elements. Creating vector time with 12222 elements. Creating vector isusTemp with 12222 elements. Creating vector time with 12222 elements. Creating vector isusQuality with 12222 elements. Creating vector time with 12222 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/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/2003/2003309/2003.309.00/biolume.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/biolume.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/biolume.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/biolume.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. Could not read from biolume.nc returning NaNs for fields. Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/lopc.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/lopc.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/lopc.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.00/lopc.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.309.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2003.309.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/ 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/2003/2003309/2003.309.01/navigation.nc') Creating vector time with 26281 elements. Creating vector mPos_x with 26281 elements. Creating vector time with 26281 elements. Creating vector mPos_y with 26281 elements. Creating vector time with 26281 elements. Creating vector mDepth with 26281 elements. Creating vector time with 26281 elements. Creating vector mGpsNorth with 26281 elements. Creating vector time with 26281 elements. Creating vector mGpsEast with 26281 elements. Creating vector time with 26281 elements. Creating vector mGpsValid with 26281 elements. Creating vector time with 26281 elements. Creating vector mPhi with 26281 elements. Creating vector time with 26281 elements. Creating vector mTheta with 26281 elements. Creating vector time with 26281 elements. Creating vector mPsi with 26281 elements. Creating vector time with 26281 elements. Creating vector mOmega_x with 26281 elements. Creating vector time with 26281 elements. Creating vector mOmega_y with 26281 elements. Creating vector time with 26281 elements. Creating vector mOmega_z with 26281 elements. Creating vector time with 26281 elements. Creating vector mPsaRange with 26281 elements. Creating vector time with 26281 elements. Creating vector mAltitude with 26281 elements. Creating vector time with 26281 elements. Creating vector mWaterSpeed with 26281 elements. Creating vector time with 26281 elements. Creating vector nfix with 26281 elements. Creating vector time with 26281 elements. Creating vector efix with 26281 elements. Creating vector time with 26281 elements. Creating vector filter_north with 26281 elements. Creating vector time with 26281 elements. Creating vector filter_east with 26281 elements. Creating vector time with 26281 elements. Creating vector filter_depth with 26281 elements. Creating vector time with 26281 elements. Creating vector north_current with 26281 elements. Creating vector time with 26281 elements. Creating vector east_current with 26281 elements. Creating vector time with 26281 elements. Creating vector speed_bias with 26281 elements. Creating vector time with 26281 elements. Creating vector heading_bias with 26281 elements. Creating vector time with 26281 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/navigation.nc'); processNav(): median of positive valued depths = 116.0717 processNav(): Finding depths less than 812.5018 and times > 0 processNav(): length(Nav.depth) = 26281 processNav(): length(gindx) = 26281 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/2003/2003309/2003.309.01/gps.nc') Creating vector time with 442 elements. Creating vector UTCTime with 442 elements. Creating vector time with 442 elements. Creating vector latitude with 442 elements. Creating vector time with 442 elements. Creating vector longitude with 442 elements. Creating vector time with 442 elements. Creating vector quality with 442 elements. Creating vector time with 442 elements. Creating vector numberOfSatellites with 442 elements. Creating vector time with 442 elements. Creating vector hdop with 442 elements. Creating vector time with 442 elements. Creating vector antennaHeight with 442 elements. Creating vector time with 442 elements. Creating vector geoHeight with 442 elements. Creating vector time with 442 elements. Creating vector dgpsDataAge with 442 elements. Creating vector time with 442 elements. Creating vector dgpsRSID with 442 elements. Creating vector time with 442 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/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/2003/2003309/2003.309.01/parosci.nc') Creating vector time with 26386 elements. Creating vector depth with 26386 elements. Creating vector time with 26386 elements. Creating vector temp with 26386 elements. Creating vector time with 26386 elements. Creating vector pressure with 26386 elements. Creating vector time with 26386 elements. Creating vector temp_period with 26386 elements. Creating vector time with 26386 elements. Creating vector pres_period with 26386 elements. Creating vector time with 26386 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.19249 max(Depth.data) = 250.9759 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.19249 max(Depth.data) = 250.9759 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/2003/2003309/2003.309.01/hydroscatlog.nc') Creating vector time with 21085 elements. Creating vector Seconds with 21085 elements. Creating vector time with 21085 elements. Creating vector HundrethsOfSeconds with 21085 elements. Creating vector time with 21085 elements. Creating vector Snorm1 with 21085 elements. Creating vector time with 21085 elements. Creating vector Snorm2 with 21085 elements. Creating vector time with 21085 elements. Creating vector Snorm3 with 21085 elements. Creating vector time with 21085 elements. Creating vector Gain_Status_1 with 21085 elements. Creating vector time with 21085 elements. Creating vector Gain_Status_2 with 21085 elements. Creating vector time with 21085 elements. Creating vector Gain_Status_3 with 21085 elements. Creating vector time with 21085 elements. Creating vector RawDepthValue with 21085 elements. Creating vector time with 21085 elements. Creating vector RawTempValue with 21085 elements. Creating vector time with 21085 elements. Creating vector Temperature with 21085 elements. Creating vector time with 21085 elements. Creating vector ErrorValue with 21085 elements. Creating vector time with 21085 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/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/2003/2003309/2003.309.01/ctdDriver.nc') Creating vector time with 21032 elements. Creating vector conductivity with 21032 elements. Creating vector time with 21032 elements. Creating vector temperature with 21032 elements. Creating vector time with 21032 elements. Creating vector cond_frequency with 21032 elements. Creating vector time with 21032 elements. Creating vector temp_frequency with 21032 elements. Creating vector time with 21032 elements. Creating vector spare with 21032 elements. Creating vector time with 21032 elements. Creating vector humidity with 21032 elements. Creating vector time with 21032 elements. Creating vector flow1 with 21032 elements. Creating vector time with 21032 elements. Creating vector OBS with 21032 elements. Creating vector time with 21032 elements. Creating vector dissolvedO2 with 21032 elements. Creating vector time with 21032 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/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/2003/2003309/2003.309.01/ctdDriver2.nc') Creating vector time with 21032 elements. Creating vector conductivity with 21032 elements. Creating vector time with 21032 elements. Creating vector temperature with 21032 elements. Creating vector time with 21032 elements. Creating vector cond_frequency with 21032 elements. Creating vector time with 21032 elements. Creating vector temp_frequency with 21032 elements. Creating vector time with 21032 elements. Creating vector flow2 with 21032 elements. Creating vector time with 21032 elements. Creating vector spare with 21032 elements. Creating vector time with 21032 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/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/2003/2003309/2003.309.01/isuslog.nc') Creating vector time with 3152 elements. Creating vector isusNitrate with 3152 elements. Creating vector time with 3152 elements. Creating vector isusTemp with 3152 elements. Creating vector time with 3152 elements. Creating vector isusQuality with 3152 elements. Creating vector time with 3152 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/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/2003/2003309/2003.309.01/biolume.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/biolume.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/biolume.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/biolume.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. Could not read from biolume.nc returning NaNs for fields. Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/lopc.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/lopc.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/lopc.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.01/lopc.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.309.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2003.309.02 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/ 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/2003/2003309/2003.309.02/navigation.nc') Creating vector time with 1888 elements. Creating vector mPos_x with 1888 elements. Creating vector time with 1888 elements. Creating vector mPos_y with 1888 elements. Creating vector time with 1888 elements. Creating vector mDepth with 1888 elements. Creating vector time with 1888 elements. Creating vector mGpsNorth with 1888 elements. Creating vector time with 1888 elements. Creating vector mGpsEast with 1888 elements. Creating vector time with 1888 elements. Creating vector mGpsValid with 1888 elements. Creating vector time with 1888 elements. Creating vector mPhi with 1888 elements. Creating vector time with 1888 elements. Creating vector mTheta with 1888 elements. Creating vector time with 1888 elements. Creating vector mPsi with 1888 elements. Creating vector time with 1888 elements. Creating vector mOmega_x with 1888 elements. Creating vector time with 1888 elements. Creating vector mOmega_y with 1888 elements. Creating vector time with 1888 elements. Creating vector mOmega_z with 1888 elements. Creating vector time with 1888 elements. Creating vector mPsaRange with 1888 elements. Creating vector time with 1888 elements. Creating vector mAltitude with 1888 elements. Creating vector time with 1888 elements. Creating vector mWaterSpeed with 1888 elements. Creating vector time with 1888 elements. Creating vector nfix with 1888 elements. Creating vector time with 1888 elements. Creating vector efix with 1888 elements. Creating vector time with 1888 elements. Creating vector filter_north with 1888 elements. Creating vector time with 1888 elements. Creating vector filter_east with 1888 elements. Creating vector time with 1888 elements. Creating vector filter_depth with 1888 elements. Creating vector time with 1888 elements. Creating vector north_current with 1888 elements. Creating vector time with 1888 elements. Creating vector east_current with 1888 elements. Creating vector time with 1888 elements. Creating vector speed_bias with 1888 elements. Creating vector time with 1888 elements. Creating vector heading_bias with 1888 elements. Creating vector time with 1888 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/navigation.nc'); processNav(): median of positive valued depths = 4.2511 processNav(): Finding depths less than 29.7576 and times > 0 processNav(): length(Nav.depth) = 1888 processNav(): length(gindx) = 1888 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/2003/2003309/2003.309.02/gps.nc') Creating vector time with 175 elements. Creating vector UTCTime with 175 elements. Creating vector time with 175 elements. Creating vector latitude with 175 elements. Creating vector time with 175 elements. Creating vector longitude with 175 elements. Creating vector time with 175 elements. Creating vector quality with 175 elements. Creating vector time with 175 elements. Creating vector numberOfSatellites with 175 elements. Creating vector time with 175 elements. Creating vector hdop with 175 elements. Creating vector time with 175 elements. Creating vector antennaHeight with 175 elements. Creating vector time with 175 elements. Creating vector geoHeight with 175 elements. Creating vector time with 175 elements. Creating vector dgpsDataAge with 175 elements. Creating vector time with 175 elements. Creating vector dgpsRSID with 175 elements. Creating vector time with 175 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/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/2003/2003309/2003.309.02/parosci.nc') Creating vector time with 1994 elements. Creating vector depth with 1994 elements. Creating vector time with 1994 elements. Creating vector temp with 1994 elements. Creating vector time with 1994 elements. Creating vector pressure with 1994 elements. Creating vector time with 1994 elements. Creating vector temp_period with 1994 elements. Creating vector time with 1994 elements. Creating vector pres_period with 1994 elements. Creating vector time with 1994 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.12785 max(Depth.data) = 6.7144 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.12785 max(Depth.data) = 6.7144 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/2003/2003309/2003.309.02/hydroscatlog.nc') Creating vector time with 1582 elements. Creating vector Seconds with 1582 elements. Creating vector time with 1582 elements. Creating vector HundrethsOfSeconds with 1582 elements. Creating vector time with 1582 elements. Creating vector Snorm1 with 1582 elements. Creating vector time with 1582 elements. Creating vector Snorm2 with 1582 elements. Creating vector time with 1582 elements. Creating vector Snorm3 with 1582 elements. Creating vector time with 1582 elements. Creating vector Gain_Status_1 with 1582 elements. Creating vector time with 1582 elements. Creating vector Gain_Status_2 with 1582 elements. Creating vector time with 1582 elements. Creating vector Gain_Status_3 with 1582 elements. Creating vector time with 1582 elements. Creating vector RawDepthValue with 1582 elements. Creating vector time with 1582 elements. Creating vector RawTempValue with 1582 elements. Creating vector time with 1582 elements. Creating vector Temperature with 1582 elements. Creating vector time with 1582 elements. Creating vector ErrorValue with 1582 elements. Creating vector time with 1582 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/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/2003/2003309/2003.309.02/ctdDriver.nc') Creating vector time with 1553 elements. Creating vector conductivity with 1553 elements. Creating vector time with 1553 elements. Creating vector temperature with 1553 elements. Creating vector time with 1553 elements. Creating vector cond_frequency with 1553 elements. Creating vector time with 1553 elements. Creating vector temp_frequency with 1553 elements. Creating vector time with 1553 elements. Creating vector spare with 1553 elements. Creating vector time with 1553 elements. Creating vector humidity with 1553 elements. Creating vector time with 1553 elements. Creating vector flow1 with 1553 elements. Creating vector time with 1553 elements. Creating vector OBS with 1553 elements. Creating vector time with 1553 elements. Creating vector dissolvedO2 with 1553 elements. Creating vector time with 1553 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/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/2003/2003309/2003.309.02/ctdDriver2.nc') Creating vector time with 1554 elements. Creating vector conductivity with 1554 elements. Creating vector time with 1554 elements. Creating vector temperature with 1554 elements. Creating vector time with 1554 elements. Creating vector cond_frequency with 1554 elements. Creating vector time with 1554 elements. Creating vector temp_frequency with 1554 elements. Creating vector time with 1554 elements. Creating vector flow2 with 1554 elements. Creating vector time with 1554 elements. Creating vector spare with 1554 elements. Creating vector time with 1554 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/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/2003/2003309/2003.309.02/isuslog.nc') Creating vector time with 196 elements. Creating vector isusNitrate with 196 elements. Creating vector time with 196 elements. Creating vector isusTemp with 196 elements. Creating vector time with 196 elements. Creating vector isusQuality with 196 elements. Creating vector time with 196 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/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/2003/2003309/2003.309.02/biolume.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/biolume.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/biolume.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/biolume.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. Could not read from biolume.nc returning NaNs for fields. Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/lopc.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/lopc.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/lopc.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.02/lopc.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.309.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2003.309.04 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/ 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/2003/2003309/2003.309.04/navigation.nc') Creating vector time with 28278 elements. Creating vector mPos_x with 28278 elements. Creating vector time with 28278 elements. Creating vector mPos_y with 28278 elements. Creating vector time with 28278 elements. Creating vector mDepth with 28278 elements. Creating vector time with 28278 elements. Creating vector mGpsNorth with 28278 elements. Creating vector time with 28278 elements. Creating vector mGpsEast with 28278 elements. Creating vector time with 28278 elements. Creating vector mGpsValid with 28278 elements. Creating vector time with 28278 elements. Creating vector mPhi with 28278 elements. Creating vector time with 28278 elements. Creating vector mTheta with 28278 elements. Creating vector time with 28278 elements. Creating vector mPsi with 28278 elements. Creating vector time with 28278 elements. Creating vector mOmega_x with 28278 elements. Creating vector time with 28278 elements. Creating vector mOmega_y with 28278 elements. Creating vector time with 28278 elements. Creating vector mOmega_z with 28278 elements. Creating vector time with 28278 elements. Creating vector mPsaRange with 28278 elements. Creating vector time with 28278 elements. Creating vector mAltitude with 28278 elements. Creating vector time with 28278 elements. Creating vector mWaterSpeed with 28278 elements. Creating vector time with 28278 elements. Creating vector nfix with 28278 elements. Creating vector time with 28278 elements. Creating vector efix with 28278 elements. Creating vector time with 28278 elements. Creating vector filter_north with 28278 elements. Creating vector time with 28278 elements. Creating vector filter_east with 28278 elements. Creating vector time with 28278 elements. Creating vector filter_depth with 28278 elements. Creating vector time with 28278 elements. Creating vector north_current with 28278 elements. Creating vector time with 28278 elements. Creating vector east_current with 28278 elements. Creating vector time with 28278 elements. Creating vector speed_bias with 28278 elements. Creating vector time with 28278 elements. Creating vector heading_bias with 28278 elements. Creating vector time with 28278 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/navigation.nc'); processNav(): median of positive valued depths = 86.4983 processNav(): Finding depths less than 605.4881 and times > 0 processNav(): length(Nav.depth) = 28278 processNav(): length(gindx) = 28278 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/2003/2003309/2003.309.04/gps.nc') Creating vector time with 619 elements. Creating vector UTCTime with 619 elements. Creating vector time with 619 elements. Creating vector latitude with 619 elements. Creating vector time with 619 elements. Creating vector longitude with 619 elements. Creating vector time with 619 elements. Creating vector quality with 619 elements. Creating vector time with 619 elements. Creating vector numberOfSatellites with 619 elements. Creating vector time with 619 elements. Creating vector hdop with 619 elements. Creating vector time with 619 elements. Creating vector antennaHeight with 619 elements. Creating vector time with 619 elements. Creating vector geoHeight with 619 elements. Creating vector time with 619 elements. Creating vector dgpsDataAge with 619 elements. Creating vector time with 619 elements. Creating vector dgpsRSID with 619 elements. Creating vector time with 619 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/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/2003/2003309/2003.309.04/parosci.nc') Creating vector time with 28385 elements. Creating vector depth with 28385 elements. Creating vector time with 28385 elements. Creating vector temp with 28385 elements. Creating vector time with 28385 elements. Creating vector pressure with 28385 elements. Creating vector time with 28385 elements. Creating vector temp_period with 28385 elements. Creating vector time with 28385 elements. Creating vector pres_period with 28385 elements. Creating vector time with 28385 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.26165 max(Depth.data) = 250.9511 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.26165 max(Depth.data) = 250.9511 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/2003/2003309/2003.309.04/hydroscatlog.nc') Creating vector time with 22684 elements. Creating vector Seconds with 22684 elements. Creating vector time with 22684 elements. Creating vector HundrethsOfSeconds with 22684 elements. Creating vector time with 22684 elements. Creating vector Snorm1 with 22684 elements. Creating vector time with 22684 elements. Creating vector Snorm2 with 22684 elements. Creating vector time with 22684 elements. Creating vector Snorm3 with 22684 elements. Creating vector time with 22684 elements. Creating vector Gain_Status_1 with 22684 elements. Creating vector time with 22684 elements. Creating vector Gain_Status_2 with 22684 elements. Creating vector time with 22684 elements. Creating vector Gain_Status_3 with 22684 elements. Creating vector time with 22684 elements. Creating vector RawDepthValue with 22684 elements. Creating vector time with 22684 elements. Creating vector RawTempValue with 22684 elements. Creating vector time with 22684 elements. Creating vector Temperature with 22684 elements. Creating vector time with 22684 elements. Creating vector ErrorValue with 22684 elements. Creating vector time with 22684 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/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/2003/2003309/2003.309.04/ctdDriver.nc') Creating vector time with 22667 elements. Creating vector conductivity with 22667 elements. Creating vector time with 22667 elements. Creating vector temperature with 22667 elements. Creating vector time with 22667 elements. Creating vector cond_frequency with 22667 elements. Creating vector time with 22667 elements. Creating vector temp_frequency with 22667 elements. Creating vector time with 22667 elements. Creating vector spare with 22667 elements. Creating vector time with 22667 elements. Creating vector humidity with 22667 elements. Creating vector time with 22667 elements. Creating vector flow1 with 22667 elements. Creating vector time with 22667 elements. Creating vector OBS with 22667 elements. Creating vector time with 22667 elements. Creating vector dissolvedO2 with 22667 elements. Creating vector time with 22667 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/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/2003/2003309/2003.309.04/ctdDriver2.nc') Creating vector time with 22666 elements. Creating vector conductivity with 22666 elements. Creating vector time with 22666 elements. Creating vector temperature with 22666 elements. Creating vector time with 22666 elements. Creating vector cond_frequency with 22666 elements. Creating vector time with 22666 elements. Creating vector temp_frequency with 22666 elements. Creating vector time with 22666 elements. Creating vector flow2 with 22666 elements. Creating vector time with 22666 elements. Creating vector spare with 22666 elements. Creating vector time with 22666 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/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/2003/2003309/2003.309.04/isuslog.nc') Creating vector time with 3395 elements. Creating vector isusNitrate with 3395 elements. Creating vector time with 3395 elements. Creating vector isusTemp with 3395 elements. Creating vector time with 3395 elements. Creating vector isusQuality with 3395 elements. Creating vector time with 3395 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/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/2003/2003309/2003.309.04/biolume.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/biolume.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/biolume.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/biolume.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. Could not read from biolume.nc returning NaNs for fields. Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/lopc.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/lopc.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/lopc.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2003/2003309/2003.309.04/lopc.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.309.04.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_2003.309.00.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.309.01.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.309.02.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.309.04.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 11 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04.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 = 70 Gridding with nix = 210, iZ = 499 Using mean boxcar filter of vector... Using mean boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Gridding... T S O Using median boxcar filter of vector... Using median boxcar filter of vector... Using median boxcar filter of vector... bbp470 bbp676 fl676_uncorr N BL Only one good point or fewer - NaNing the gBL array. BLflow Only one good point or fewer - NaNing the gBLflow array. LOPC Only one good point or fewer - NaNing the gLOPCcount array. - NaNing the gLOPCtransCount array. - NaNing the gLOPCnonTransCount array. - NaNing the gLOPCLCcount array. Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB470 cvarname = gB676 cvarname = gBL No valid data for gBL cvarname = gBLflow No valid data for gBLflow cvarname = gLOPCcount No valid data for gLOPCcount cvarname = gLOPCtransCount No valid data for gLOPCtransCount cvarname = gLOPCnonTransCount No valid data for gLOPCnonTransCount cvarname = gLOPCLCcount No valid data for gLOPCLCcount Encountered 0 NaN values in array of lon that is 138273 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 138273 points from grid Monterey25.grd (2876 x 2447) Executing: /bin/rm -f ../results/2003309_GulperTimes.txt && touch ../results/2003309_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/2003/2003309/2003.309.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003309/2003.309.00/syslog -startEsecs 1068032007.4249 -surveyName Dorado389_2003_309_00_309_04 >> ../results/2003309_GulperTimes.txt Executing: removeGulpDups.py ../results/2003309_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/2003/2003309/2003.309.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003309/2003.309.01/syslog -startEsecs 1068032007.4249 -surveyName Dorado389_2003_309_00_309_04 >> ../results/2003309_GulperTimes.txt Executing: removeGulpDups.py ../results/2003309_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/2003/2003309/2003.309.02/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003309/2003.309.02/syslog -startEsecs 1068032007.4249 -surveyName Dorado389_2003_309_00_309_04 >> ../results/2003309_GulperTimes.txt Executing: removeGulpDups.py ../results/2003309_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/2003/2003309/2003.309.04/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2003/2003309/2003.309.04/syslog -startEsecs 1068032007.4249 -surveyName Dorado389_2003_309_00_309_04 >> ../results/2003309_GulperTimes.txt Executing: removeGulpDups.py ../results/2003309_GulperTimes.txt Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_gridded.mat outvarstr = 'gF gT gN gS gD gO gB470 gB676 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth ' 2Column contouring gridded variable gD 2Column contouring gridded variable gT 2Column contouring gridded variable gS 2Column contouring gridded variable gN 2Column contouring gridded variable gO 2Column contouring gridded variable gB470 2Column contouring gridded variable gB676 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_2column.png Elapsed time to save image: 6 seconds Biolume contouring gridded variable gD Biolume contouring gridded variable gT Biolume contouring gridded variable gS Biolume contouring gridded variable gN Biolume contouring gridded variable gO Biolume contouring gridded variable gB470 Biolume contouring gridded variable gB676 Biolume contouring gridded variable gF Biolume contouring gridded variable gBL Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_biolume.png Elapsed time to save image: 30 seconds 2Column contouring gridded variable gLOPCcount 2Column contouring gridded variable gLOPCtransCount 2Column contouring gridded variable gLOPCnonTransCount 2Column contouring gridded variable gLOPCLCcount 2Column contouring gridded variable gT 2Column contouring gridded variable gB470 2Column contouring gridded variable gB676 2Column contouring gridded variable gF 2Column contouring gridded variable gBL Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_lopc.png Elapsed time to save image: 6 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_2003_309_00_309_04_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_2column.png... Copied to /mbari/AUVCTD/surveys/2003/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_biolume.png... Copied to /mbari/AUVCTD/surveys/2003/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_lopc.png... Copied to /mbari/AUVCTD/surveys/2003/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2003/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2003/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2003/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_2003_309_00_309_04_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2003/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_2003_309_00_309_04_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2003/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_2003_309_00_309_04_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2003/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_2003_309_00_309_04_Oxygen.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @470 nm', jetplus, varlimits(5,:), hs2.bbp470, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Optical_Backscatter_470_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Optical_Backscatter_470_nm.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Optical_Backscatter_676_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Optical_Backscatter_676_nm.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); length(v_esecs(gindx)) = which is less than 2. Not processing. adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Bioluminescence.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath); length(v_esecs(gindx)) = which is less than 2. Not processing. adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2003_309_00_309_04.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04.kml... Copied to /mbari/AUVCTD/surveys/2003/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2003_309_00_309_04_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_2003_309_00_309_04.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Encountered 2343 NaN values in array of lon that is 18965 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 16622 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 16622 are not equal to number of Lat lon points = 18965 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_2003_309_00_309_04.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04.txt... Copied to /mbari/AUVCTD/surveys/2003/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_Gulper.txt... Tried, but failed to copy to /mbari/AUVCTD/surveys/2003/odv/ cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_Gulper.txt’: No such file or directory ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_decim.nc... Copied to /mbari/AUVCTD/surveys/2003/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_2003_309_00_309_04.nc... Copied to /mbari/AUVCTD/surveys/2003/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04_gridded.mat... Copied to /mbari/AUVCTD/surveys/2003/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003_309_00_309_04.mat... Copied to /mbari/AUVCTD/surveys/2003/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2003_309_00_309_04 processed" mccann@mbari.org < mail_Dorado389_2003_309_00_309_04.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.309.00.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.309.01.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.309.02.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2003.309.04.mat Processing time: 177 seconds