Execution of AUVprocess_main version 1.86 at 2018-06-01T22:00:03Z on elvis Matlab command executed: AUVprocess_main('OCCO', 2004, ['344.05';'344.06';'344.07'], '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: 2004.344.05 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.05/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.05/ 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/2004/2004344/2004.344.05/navigation.nc') Creating vector time with 56686 elements. Creating vector mPos_x with 56686 elements. Creating vector time with 56686 elements. Creating vector mPos_y with 56686 elements. Creating vector time with 56686 elements. Creating vector mDepth with 56686 elements. Creating vector time with 56686 elements. Creating vector mGpsNorth with 56686 elements. Creating vector time with 56686 elements. Creating vector mGpsEast with 56686 elements. Creating vector time with 56686 elements. Creating vector mGpsValid with 56686 elements. Creating vector time with 56686 elements. Creating vector mPhi with 56686 elements. Creating vector time with 56686 elements. Creating vector mTheta with 56686 elements. Creating vector time with 56686 elements. Creating vector mPsi with 56686 elements. Creating vector time with 56686 elements. Creating vector mOmega_x with 56686 elements. Creating vector time with 56686 elements. Creating vector mOmega_y with 56686 elements. Creating vector time with 56686 elements. Creating vector mOmega_z with 56686 elements. Creating vector time with 56686 elements. Creating vector mPsaRange with 56686 elements. Creating vector time with 56686 elements. Creating vector mAltitude with 56686 elements. Creating vector time with 56686 elements. Creating vector mWaterSpeed with 56686 elements. Creating vector time with 56686 elements. Creating vector mDvlValid with 56686 elements. Creating vector time with 56686 elements. Creating vector mDvlNewData with 56686 elements. Creating vector time with 56686 elements. Creating vector mDeltaT with 56686 elements. Creating vector time with 56686 elements. Creating vector latitude with 56686 elements. Creating vector time with 56686 elements. Creating vector longitude with 56686 elements. Creating vector time with 56686 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.05/navigation.nc'); processNav(): median of positive valued depths = 9.2228 processNav(): Finding depths less than 64.5597 and times > 0 processNav(): length(Nav.depth) = 56686 processNav(): length(gindx) = 56686 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/2004/2004344/2004.344.05/gps.nc') Creating vector time with 672 elements. Creating vector hours with 672 elements. Creating vector time with 672 elements. Creating vector minutes with 672 elements. Creating vector time with 672 elements. Creating vector seconds with 672 elements. Creating vector time with 672 elements. Creating vector centiSeconds with 672 elements. Creating vector time with 672 elements. Creating vector latitude with 672 elements. Creating vector time with 672 elements. Creating vector longitude with 672 elements. Creating vector time with 672 elements. Creating vector quality with 672 elements. Creating vector time with 672 elements. Creating vector numberOfSatellites with 672 elements. Creating vector time with 672 elements. Creating vector hdop with 672 elements. Creating vector time with 672 elements. Creating vector antennaHeight with 672 elements. Creating vector time with 672 elements. Creating vector geoHeight with 672 elements. Creating vector time with 672 elements. Creating vector dgpsDataAge with 672 elements. Creating vector time with 672 elements. Creating vector dgpsRSID with 672 elements. Creating vector time with 672 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/parosci.nc') Creating vector time with 56792 elements. Creating vector depth with 56792 elements. Creating vector time with 56792 elements. Creating vector temp with 56792 elements. Creating vector time with 56792 elements. Creating vector pressure with 56792 elements. Creating vector time with 56792 elements. Creating vector temp_period with 56792 elements. Creating vector time with 56792 elements. Creating vector pres_period with 56792 elements. Creating vector time with 56792 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.05/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.2672 max(Depth.data) = 16.9541 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.2672 max(Depth.data) = 16.9541 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/2004/2004344/2004.344.05/hydroscatlog.nc') Creating vector time with 45399 elements. Creating vector Seconds with 45399 elements. Creating vector time with 45399 elements. Creating vector HundrethsOfSeconds with 45399 elements. Creating vector time with 45399 elements. Creating vector Snorm1 with 45399 elements. Creating vector time with 45399 elements. Creating vector Snorm2 with 45399 elements. Creating vector time with 45399 elements. Creating vector Snorm3 with 45399 elements. Creating vector time with 45399 elements. Creating vector Gain_Status_1 with 45399 elements. Creating vector time with 45399 elements. Creating vector Gain_Status_2 with 45399 elements. Creating vector time with 45399 elements. Creating vector Gain_Status_3 with 45399 elements. Creating vector time with 45399 elements. Creating vector RawDepthValue with 45399 elements. Creating vector time with 45399 elements. Creating vector RawTempValue with 45399 elements. Creating vector time with 45399 elements. Creating vector Temperature with 45399 elements. Creating vector time with 45399 elements. Creating vector ErrorValue with 45399 elements. Creating vector time with 45399 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/ctdDriver.nc') Creating vector time with 45331 elements. Creating vector conductivity with 45331 elements. Creating vector time with 45331 elements. Creating vector temperature with 45331 elements. Creating vector time with 45331 elements. Creating vector cond_frequency with 45331 elements. Creating vector time with 45331 elements. Creating vector temp_frequency with 45331 elements. Creating vector time with 45331 elements. Creating vector spare with 45331 elements. Creating vector time with 45331 elements. Creating vector humidity with 45331 elements. Creating vector time with 45331 elements. Creating vector flow1 with 45331 elements. Creating vector time with 45331 elements. Creating vector OBS with 45331 elements. Creating vector time with 45331 elements. Creating vector dissolvedO2 with 45331 elements. Creating vector time with 45331 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.05/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/ctdDriver2.nc') Creating vector time with 44585 elements. Creating vector conductivity with 44585 elements. Creating vector time with 44585 elements. Creating vector temperature with 44585 elements. Creating vector time with 44585 elements. Creating vector cond_frequency with 44585 elements. Creating vector time with 44585 elements. Creating vector temp_frequency with 44585 elements. Creating vector time with 44585 elements. Creating vector flow2 with 44585 elements. Creating vector time with 44585 elements. Creating vector spare with 44585 elements. Creating vector time with 44585 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.05/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/isuslog.nc') Creating vector time with 7287 elements. Creating vector isusNitrate with 7287 elements. Creating vector time with 7287 elements. Creating vector isusTemp with 7287 elements. Creating vector time with 7287 elements. Creating vector isusQuality with 7287 elements. Creating vector time with 7287 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/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/2004/2004344/2004.344.05/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_2004.344.05.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2004.344.06 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.06/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.06/ 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/2004/2004344/2004.344.06/navigation.nc') Creating vector time with 57695 elements. Creating vector mPos_x with 57695 elements. Creating vector time with 57695 elements. Creating vector mPos_y with 57695 elements. Creating vector time with 57695 elements. Creating vector mDepth with 57695 elements. Creating vector time with 57695 elements. Creating vector mGpsNorth with 57695 elements. Creating vector time with 57695 elements. Creating vector mGpsEast with 57695 elements. Creating vector time with 57695 elements. Creating vector mGpsValid with 57695 elements. Creating vector time with 57695 elements. Creating vector mPhi with 57695 elements. Creating vector time with 57695 elements. Creating vector mTheta with 57695 elements. Creating vector time with 57695 elements. Creating vector mPsi with 57695 elements. Creating vector time with 57695 elements. Creating vector mOmega_x with 57695 elements. Creating vector time with 57695 elements. Creating vector mOmega_y with 57695 elements. Creating vector time with 57695 elements. Creating vector mOmega_z with 57695 elements. Creating vector time with 57695 elements. Creating vector mPsaRange with 57695 elements. Creating vector time with 57695 elements. Creating vector mAltitude with 57695 elements. Creating vector time with 57695 elements. Creating vector mWaterSpeed with 57695 elements. Creating vector time with 57695 elements. Creating vector mDvlValid with 57695 elements. Creating vector time with 57695 elements. Creating vector mDvlNewData with 57695 elements. Creating vector time with 57695 elements. Creating vector mDeltaT with 57695 elements. Creating vector time with 57695 elements. Creating vector latitude with 57695 elements. Creating vector time with 57695 elements. Creating vector longitude with 57695 elements. Creating vector time with 57695 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.06/navigation.nc'); processNav(): median of positive valued depths = 8.6597 processNav(): Finding depths less than 60.6176 and times > 0 processNav(): length(Nav.depth) = 57695 processNav(): length(gindx) = 57695 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/2004/2004344/2004.344.06/gps.nc') Creating vector time with 529 elements. Creating vector hours with 529 elements. Creating vector time with 529 elements. Creating vector minutes with 529 elements. Creating vector time with 529 elements. Creating vector seconds with 529 elements. Creating vector time with 529 elements. Creating vector centiSeconds with 529 elements. Creating vector time with 529 elements. Creating vector latitude with 529 elements. Creating vector time with 529 elements. Creating vector longitude with 529 elements. Creating vector time with 529 elements. Creating vector quality with 529 elements. Creating vector time with 529 elements. Creating vector numberOfSatellites with 529 elements. Creating vector time with 529 elements. Creating vector hdop with 529 elements. Creating vector time with 529 elements. Creating vector antennaHeight with 529 elements. Creating vector time with 529 elements. Creating vector geoHeight with 529 elements. Creating vector time with 529 elements. Creating vector dgpsDataAge with 529 elements. Creating vector time with 529 elements. Creating vector dgpsRSID with 529 elements. Creating vector time with 529 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/parosci.nc') Creating vector time with 57764 elements. Creating vector depth with 57764 elements. Creating vector time with 57764 elements. Creating vector temp with 57764 elements. Creating vector time with 57764 elements. Creating vector pressure with 57764 elements. Creating vector time with 57764 elements. Creating vector temp_period with 57764 elements. Creating vector time with 57764 elements. Creating vector pres_period with 57764 elements. Creating vector time with 57764 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.06/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.24167 max(Depth.data) = 16.3969 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.24167 max(Depth.data) = 16.3969 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/2004/2004344/2004.344.06/hydroscatlog.nc') Creating vector time with 46197 elements. Creating vector Seconds with 46197 elements. Creating vector time with 46197 elements. Creating vector HundrethsOfSeconds with 46197 elements. Creating vector time with 46197 elements. Creating vector Snorm1 with 46197 elements. Creating vector time with 46197 elements. Creating vector Snorm2 with 46197 elements. Creating vector time with 46197 elements. Creating vector Snorm3 with 46197 elements. Creating vector time with 46197 elements. Creating vector Gain_Status_1 with 46197 elements. Creating vector time with 46197 elements. Creating vector Gain_Status_2 with 46197 elements. Creating vector time with 46197 elements. Creating vector Gain_Status_3 with 46197 elements. Creating vector time with 46197 elements. Creating vector RawDepthValue with 46197 elements. Creating vector time with 46197 elements. Creating vector RawTempValue with 46197 elements. Creating vector time with 46197 elements. Creating vector Temperature with 46197 elements. Creating vector time with 46197 elements. Creating vector ErrorValue with 46197 elements. Creating vector time with 46197 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/ctdDriver.nc') Creating vector time with 46163 elements. Creating vector conductivity with 46163 elements. Creating vector time with 46163 elements. Creating vector temperature with 46163 elements. Creating vector time with 46163 elements. Creating vector cond_frequency with 46163 elements. Creating vector time with 46163 elements. Creating vector temp_frequency with 46163 elements. Creating vector time with 46163 elements. Creating vector spare with 46163 elements. Creating vector time with 46163 elements. Creating vector humidity with 46163 elements. Creating vector time with 46163 elements. Creating vector flow1 with 46163 elements. Creating vector time with 46163 elements. Creating vector OBS with 46163 elements. Creating vector time with 46163 elements. Creating vector dissolvedO2 with 46163 elements. Creating vector time with 46163 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.06/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/ctdDriver2.nc') Creating vector time with 46182 elements. Creating vector conductivity with 46182 elements. Creating vector time with 46182 elements. Creating vector temperature with 46182 elements. Creating vector time with 46182 elements. Creating vector cond_frequency with 46182 elements. Creating vector time with 46182 elements. Creating vector temp_frequency with 46182 elements. Creating vector time with 46182 elements. Creating vector flow2 with 46182 elements. Creating vector time with 46182 elements. Creating vector spare with 46182 elements. Creating vector time with 46182 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.06/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/isuslog.nc') Creating vector time with 7411 elements. Creating vector isusNitrate with 7411 elements. Creating vector time with 7411 elements. Creating vector isusTemp with 7411 elements. Creating vector time with 7411 elements. Creating vector isusQuality with 7411 elements. Creating vector time with 7411 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/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/2004/2004344/2004.344.06/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_2004.344.06.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2004.344.07 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.07/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.07/ 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/2004/2004344/2004.344.07/navigation.nc') Creating vector time with 19212 elements. Creating vector mPos_x with 19212 elements. Creating vector time with 19212 elements. Creating vector mPos_y with 19212 elements. Creating vector time with 19212 elements. Creating vector mDepth with 19212 elements. Creating vector time with 19212 elements. Creating vector mGpsNorth with 19212 elements. Creating vector time with 19212 elements. Creating vector mGpsEast with 19212 elements. Creating vector time with 19212 elements. Creating vector mGpsValid with 19212 elements. Creating vector time with 19212 elements. Creating vector mPhi with 19212 elements. Creating vector time with 19212 elements. Creating vector mTheta with 19212 elements. Creating vector time with 19212 elements. Creating vector mPsi with 19212 elements. Creating vector time with 19212 elements. Creating vector mOmega_x with 19212 elements. Creating vector time with 19212 elements. Creating vector mOmega_y with 19212 elements. Creating vector time with 19212 elements. Creating vector mOmega_z with 19212 elements. Creating vector time with 19212 elements. Creating vector mPsaRange with 19212 elements. Creating vector time with 19212 elements. Creating vector mAltitude with 19212 elements. Creating vector time with 19212 elements. Creating vector mWaterSpeed with 19212 elements. Creating vector time with 19212 elements. Creating vector mDvlValid with 19212 elements. Creating vector time with 19212 elements. Creating vector mDvlNewData with 19212 elements. Creating vector time with 19212 elements. Creating vector mDeltaT with 19212 elements. Creating vector time with 19212 elements. Creating vector latitude with 19212 elements. Creating vector time with 19212 elements. Creating vector longitude with 19212 elements. Creating vector time with 19212 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.07/navigation.nc'); processNav(): median of positive valued depths = 8.4235 processNav(): Finding depths less than 58.9644 and times > 0 processNav(): length(Nav.depth) = 19212 processNav(): length(gindx) = 19212 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/2004/2004344/2004.344.07/gps.nc') Creating vector time with 218 elements. Creating vector hours with 218 elements. Creating vector time with 218 elements. Creating vector minutes with 218 elements. Creating vector time with 218 elements. Creating vector seconds with 218 elements. Creating vector time with 218 elements. Creating vector centiSeconds with 218 elements. Creating vector time with 218 elements. Creating vector latitude with 218 elements. Creating vector time with 218 elements. Creating vector longitude with 218 elements. Creating vector time with 218 elements. Creating vector quality with 218 elements. Creating vector time with 218 elements. Creating vector numberOfSatellites with 218 elements. Creating vector time with 218 elements. Creating vector hdop with 218 elements. Creating vector time with 218 elements. Creating vector antennaHeight with 218 elements. Creating vector time with 218 elements. Creating vector geoHeight with 218 elements. Creating vector time with 218 elements. Creating vector dgpsDataAge with 218 elements. Creating vector time with 218 elements. Creating vector dgpsRSID with 218 elements. Creating vector time with 218 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/parosci.nc') Creating vector time with 19311 elements. Creating vector depth with 19311 elements. Creating vector time with 19311 elements. Creating vector temp with 19311 elements. Creating vector time with 19311 elements. Creating vector pressure with 19311 elements. Creating vector time with 19311 elements. Creating vector temp_period with 19311 elements. Creating vector time with 19311 elements. Creating vector pres_period with 19311 elements. Creating vector time with 19311 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.07/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.20459 max(Depth.data) = 17.1174 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.20459 max(Depth.data) = 17.1174 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/2004/2004344/2004.344.07/hydroscatlog.nc') Creating vector time with 15425 elements. Creating vector Seconds with 15425 elements. Creating vector time with 15425 elements. Creating vector HundrethsOfSeconds with 15425 elements. Creating vector time with 15425 elements. Creating vector Snorm1 with 15425 elements. Creating vector time with 15425 elements. Creating vector Snorm2 with 15425 elements. Creating vector time with 15425 elements. Creating vector Snorm3 with 15425 elements. Creating vector time with 15425 elements. Creating vector Gain_Status_1 with 15425 elements. Creating vector time with 15425 elements. Creating vector Gain_Status_2 with 15425 elements. Creating vector time with 15425 elements. Creating vector Gain_Status_3 with 15425 elements. Creating vector time with 15425 elements. Creating vector RawDepthValue with 15425 elements. Creating vector time with 15425 elements. Creating vector RawTempValue with 15425 elements. Creating vector time with 15425 elements. Creating vector Temperature with 15425 elements. Creating vector time with 15425 elements. Creating vector ErrorValue with 15425 elements. Creating vector time with 15425 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/ctdDriver.nc') Creating vector time with 15375 elements. Creating vector conductivity with 15375 elements. Creating vector time with 15375 elements. Creating vector temperature with 15375 elements. Creating vector time with 15375 elements. Creating vector cond_frequency with 15375 elements. Creating vector time with 15375 elements. Creating vector temp_frequency with 15375 elements. Creating vector time with 15375 elements. Creating vector spare with 15375 elements. Creating vector time with 15375 elements. Creating vector humidity with 15375 elements. Creating vector time with 15375 elements. Creating vector flow1 with 15375 elements. Creating vector time with 15375 elements. Creating vector OBS with 15375 elements. Creating vector time with 15375 elements. Creating vector dissolvedO2 with 15375 elements. Creating vector time with 15375 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.07/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/ctdDriver2.nc') Creating vector time with 15403 elements. Creating vector conductivity with 15403 elements. Creating vector time with 15403 elements. Creating vector temperature with 15403 elements. Creating vector time with 15403 elements. Creating vector cond_frequency with 15403 elements. Creating vector time with 15403 elements. Creating vector temp_frequency with 15403 elements. Creating vector time with 15403 elements. Creating vector flow2 with 15403 elements. Creating vector time with 15403 elements. Creating vector spare with 15403 elements. Creating vector time with 15403 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.07/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/isuslog.nc') Creating vector time with 2452 elements. Creating vector isusNitrate with 2452 elements. Creating vector time with 2452 elements. Creating vector isusTemp with 2452 elements. Creating vector time with 2452 elements. Creating vector isusQuality with 2452 elements. Creating vector time with 2452 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/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/2004/2004344/2004.344.07/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_2004.344.07.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_2004.344.05.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.344.06.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.344.07.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 21 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07.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 = 282 Gridding with nix = 846, iZ = 31 Using mean boxcar filter of vector... Using mean boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Gridding... T S O Using median boxcar filter of vector... Using median boxcar filter of vector... Using median boxcar filter of vector... bbp470 [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 231) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] bbp676 [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 253) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] fl676_uncorr [Warning: Duplicate data points have been detected and removed - corresponding values have been averaged.] [> In griddata>useScatteredInterp (line 185) In griddata (line 126) In plot_sections (line 274) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 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 133497 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 133497 points from grid Monterey25.grd (2876 x 2447) Executing: /bin/rm -f ../results/2004344_GulperTimes.txt && touch ../results/2004344_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/2004/2004344/2004.344.05/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004344/2004.344.05/syslog -startEsecs 1102633043.4053 -surveyName Dorado389_2004_344_05_344_07 >> ../results/2004344_GulperTimes.txt Executing: removeGulpDups.py ../results/2004344_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/2004/2004344/2004.344.06/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004344/2004.344.06/syslog -startEsecs 1102633043.4053 -surveyName Dorado389_2004_344_05_344_07 >> ../results/2004344_GulperTimes.txt Executing: removeGulpDups.py ../results/2004344_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/2004/2004344/2004.344.07/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004344/2004.344.07/syslog -startEsecs 1102633043.4053 -surveyName Dorado389_2004_344_05_344_07 >> ../results/2004344_GulperTimes.txt Executing: removeGulpDups.py ../results/2004344_GulperTimes.txt Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_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_2004_344_05_344_07_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_2004_344_05_344_07_biolume.png Elapsed time to save image: 29 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_2004_344_05_344_07_lopc.png Elapsed time to save image: 5 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_2column.png... Copied to /mbari/AUVCTD/surveys/2004/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_biolume.png... Copied to /mbari/AUVCTD/surveys/2004/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_lopc.png... Copied to /mbari/AUVCTD/surveys/2004/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2004/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2004/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2004/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_2004_344_05_344_07_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_344_05_344_07_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2004/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_2004_344_05_344_07_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_344_05_344_07_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2004/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_2004_344_05_344_07_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_344_05_344_07_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2004/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_2004_344_05_344_07_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_344_05_344_07_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2004/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @470 nm', jetplus, varlimits(5,:), hs2.bbp470, time.hs2, auvnav, depth.hs2, resultspath); Could not do interp1: The grid vectors must contain unique points. Did not write KML for this variable. Rethrowing error. Could not create .kmz for Optical Backscatter @470 nm KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath); Could not do interp1: The grid vectors must contain unique points. Did not write KML for this variable. Rethrowing error. Could not create .kmz for Optical Backscatter @676 nm KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath); Could not do interp1: The grid vectors must contain unique points. Did not write KML for this variable. Rethrowing error. Could not create .kmz for Chlorophyll Fluorescence KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); length(v_esecs(gindx)) = which is less than 2. Not processing. adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_344_05_344_07_Bioluminescence.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_344_05_344_07_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2004/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_2004_344_05_344_07_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_344_05_344_07_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2004/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2004_344_05_344_07.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07.kml... Copied to /mbari/AUVCTD/surveys/2004/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_344_05_344_07_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_2004_344_05_344_07.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 135 NaNs found in bbpBlue. Interpolating anyway. 196 NaNs found in bbpRed. Interpolating anyway. Encountered 15 NaN values in array of lon that is 17150 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 17135 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 17135 are not equal to number of Lat lon points = 17150 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_2004_344_05_344_07.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07.txt... Copied to /mbari/AUVCTD/surveys/2004/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_Gulper.txt... Tried, but failed to copy to /mbari/AUVCTD/surveys/2004/odv/ cp: cannot stat ‘/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_Gulper.txt’: No such file or directory ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 135 NaNs found in bbpBlue. Interpolating anyway. 196 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_decim.nc... Copied to /mbari/AUVCTD/surveys/2004/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_2004_344_05_344_07.nc... Copied to /mbari/AUVCTD/surveys/2004/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07_gridded.mat... Copied to /mbari/AUVCTD/surveys/2004/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_344_05_344_07.mat... Copied to /mbari/AUVCTD/surveys/2004/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2004_344_05_344_07 processed" mccann@mbari.org < mail_Dorado389_2004_344_05_344_07.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.344.05.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.344.06.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.344.07.mat Processing time: 115 seconds