Execution of AUVprocess_main version 1.84 at 2010-07-01T20:46:04Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2010, ['181.01';'181.02'], 'ssds.shore.mbari.org', 2, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2010.181.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/navigation.nc') Creating vector time with 9158 elements. Creating vector mPos_x with 9158 elements. Creating vector time with 9158 elements. Creating vector mPos_y with 9158 elements. Creating vector time with 9158 elements. Creating vector mDepth with 9158 elements. Creating vector time with 9158 elements. Creating vector mGpsNorth with 9158 elements. Creating vector time with 9158 elements. Creating vector mGpsEast with 9158 elements. Creating vector time with 9158 elements. Creating vector mGpsValid with 9158 elements. Creating vector time with 9158 elements. Creating vector mPhi with 9158 elements. Creating vector time with 9158 elements. Creating vector mTheta with 9158 elements. Creating vector time with 9158 elements. Creating vector mPsi with 9158 elements. Creating vector time with 9158 elements. Creating vector mOmega_x with 9158 elements. Creating vector time with 9158 elements. Creating vector mOmega_y with 9158 elements. Creating vector time with 9158 elements. Creating vector mOmega_z with 9158 elements. Creating vector time with 9158 elements. Creating vector mPsaRange with 9158 elements. Creating vector time with 9158 elements. Creating vector mAltitude with 9158 elements. Creating vector time with 9158 elements. Creating vector mDvlAltitude with 9158 elements. Creating vector time with 9158 elements. Creating vector mWaterSpeed with 9158 elements. Creating vector time with 9158 elements. Creating vector mDvlValid with 9158 elements. Creating vector time with 9158 elements. Creating vector mDvlNewData with 9158 elements. Creating vector time with 9158 elements. Creating vector mDeltaT with 9158 elements. Creating vector time with 9158 elements. Creating vector nfix with 9158 elements. Creating vector time with 9158 elements. Creating vector efix with 9158 elements. Creating vector time with 9158 elements. Creating vector filter_north with 9158 elements. Creating vector time with 9158 elements. Creating vector filter_east with 9158 elements. Creating vector time with 9158 elements. Creating vector filter_depth with 9158 elements. Creating vector time with 9158 elements. Creating vector north_current with 9158 elements. Creating vector time with 9158 elements. Creating vector east_current with 9158 elements. Creating vector time with 9158 elements. Creating vector speed_bias with 9158 elements. Creating vector time with 9158 elements. Creating vector heading_bias with 9158 elements. Creating vector time with 9158 elements. Creating vector latitude with 9158 elements. Creating vector time with 9158 elements. Creating vector longitude with 9158 elements. Creating vector time with 9158 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/navigation.nc'); processNav(): median of depths = 6.7755 processNav(): Finding good depths less than 677.5464 processNav(): length(Nav.depth) = 9158 processNav(): length(gindx) = 9158 java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/navigation.nc_nav_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/navigation.nc_nav_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/navigation.nc_nav_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37595 updated. Processing GPS navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/gps.nc') Creating vector time with 626 elements. Creating vector hours with 626 elements. Creating vector time with 626 elements. Creating vector minutes with 626 elements. Creating vector time with 626 elements. Creating vector seconds with 626 elements. Creating vector time with 626 elements. Creating vector centiSeconds with 626 elements. Creating vector time with 626 elements. Creating vector latitude with 626 elements. Creating vector time with 626 elements. Creating vector longitude with 626 elements. Creating vector time with 626 elements. Creating vector quality with 626 elements. Creating vector time with 626 elements. Creating vector numberOfSatellites with 626 elements. Creating vector time with 626 elements. Creating vector hdop with 626 elements. Creating vector time with 626 elements. Creating vector antennaHeight with 626 elements. Creating vector time with 626 elements. Creating vector geoHeight with 626 elements. Creating vector time with 626 elements. Creating vector dgpsDataAge with 626 elements. Creating vector time with 626 elements. Creating vector dgpsRSID with 626 elements. Creating vector time with 626 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/gps.nc'); java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/gps.nc_gps_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/gps.nc_gps_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/gps.nc_gps_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37596 updated. Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/parosci.nc') Creating vector time with 15260 elements. Creating vector depth with 15260 elements. Creating vector time with 15260 elements. Creating vector temp with 15260 elements. Creating vector time with 15260 elements. Creating vector pressure with 15260 elements. Creating vector time with 15260 elements. Creating vector temp_period with 15260 elements. Creating vector time with 15260 elements. Creating vector pres_period with 15260 elements. Creating vector time with 15260 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.18702 max(Depth.data) = 23.5196 Found 3411 bad (> 300 | < 0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = 1.5277e-05 max(Depth.data) = 23.5196 java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/parosci.nc_depth_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/parosci.nc_depth_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/parosci.nc_depth_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37597 updated. Processing hs2 backscattering and chlorophyll fluorescence data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/hydroscatlog.nc') Creating vector time with 7474 elements. Creating vector Seconds with 7474 elements. Creating vector time with 7474 elements. Creating vector HundrethsOfSeconds with 7474 elements. Creating vector time with 7474 elements. Creating vector Snorm1 with 7474 elements. Creating vector time with 7474 elements. Creating vector Snorm2 with 7474 elements. Creating vector time with 7474 elements. Creating vector Snorm3 with 7474 elements. Creating vector time with 7474 elements. Creating vector Gain_Status_1 with 7474 elements. Creating vector time with 7474 elements. Creating vector Gain_Status_2 with 7474 elements. Creating vector time with 7474 elements. Creating vector Gain_Status_3 with 7474 elements. Creating vector time with 7474 elements. Creating vector RawDepthValue with 7474 elements. Creating vector time with 7474 elements. Creating vector RawTempValue with 7474 elements. Creating vector time with 7474 elements. Creating vector Temperature with 7474 elements. Creating vector time with 7474 elements. Creating vector ErrorValue with 7474 elements. Creating vector time with 7474 elements. Creating vector bb470 with 7474 elements. Creating vector time with 7474 elements. Creating vector bb676 with 7474 elements. Creating vector time with 7474 elements. Creating vector fl676u with 7474 elements. Creating vector time with 7474 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/hydroscatlog.nc'); {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In processHS2 at 65 In processAUVmission at 128 In AUVprocess_main at 219 In reprocess_surveys at 951 java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/hydroscatlog.nc_hs2_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/hydroscatlog.nc_hs2_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/hydroscatlog.nc_hs2_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37598 updated. Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/ctdDriver.nc') Creating vector time with 7263 elements. Creating vector conductivity with 7263 elements. Creating vector time with 7263 elements. Creating vector temperature with 7263 elements. Creating vector time with 7263 elements. Creating vector cond_frequency with 7263 elements. Creating vector time with 7263 elements. Creating vector temp_frequency with 7263 elements. Creating vector time with 7263 elements. Creating vector spare with 7263 elements. Creating vector time with 7263 elements. Creating vector humidity with 7263 elements. Creating vector time with 7263 elements. Creating vector flow1 with 7263 elements. Creating vector time with 7263 elements. Creating vector rhodamine with 7263 elements. Creating vector time with 7263 elements. Creating vector dissolvedO2 with 7263 elements. Creating vector time with 7263 elements. Creating vector salinity with 7263 elements. Creating vector time with 7263 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/ctdDriver.cfg {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In processCTD at 48 In processAUVmission at 151 In AUVprocess_main at 219 In reprocess_surveys at 951 Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver.nc_ctd_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver.nc_ctd_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver.nc_ctd_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37599 updated. Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/ctdDriver2.nc') Creating vector time with 7396 elements. Creating vector conductivity with 7396 elements. Creating vector time with 7396 elements. Creating vector temperature with 7396 elements. Creating vector time with 7396 elements. Creating vector cond_frequency with 7396 elements. Creating vector time with 7396 elements. Creating vector temp_frequency with 7396 elements. Creating vector time with 7396 elements. Creating vector flow2 with 7396 elements. Creating vector time with 7396 elements. Creating vector spare with 7396 elements. Creating vector time with 7396 elements. Creating vector salinity with 7396 elements. Creating vector time with 7396 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/ctdDriver2.cfg {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In processCTD at 48 In processAUVmission at 173 In AUVprocess_main at 219 In reprocess_surveys at 951 java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver2.nc_ctd2_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver2.nc_ctd2_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver2.nc_ctd2_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37600 updated. Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/isuslog.nc') Creating vector time with 1409 elements. Creating vector isusNitrate with 1409 elements. Creating vector time with 1409 elements. Creating vector isusTemp with 1409 elements. Creating vector time with 1409 elements. Creating vector isusQuality with 1409 elements. Creating vector time with 1409 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/isuslog.nc'); Total lag applied to nitrate = 6 seconds {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In processISUS at 22 In processAUVmission at 196 In AUVprocess_main at 219 In reprocess_surveys at 951 java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/isuslog.nc_isus_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/isuslog.nc_isus_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/isuslog.nc_isus_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37601 updated. Processing Biolume data... {Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.} > In rmpath at 58 In processBiolume at 21 In processAUVmission at 219 In AUVprocess_main at 219 In reprocess_surveys at 951 loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/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/2010/2010181/2010.181.01/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/2010/2010181/2010.181.01/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/2010/2010181/2010.181.01/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/2010/2010181/2010.181.01/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/2010/2010181/2010.181.01/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/2010/2010181/2010.181.01/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/2010/2010181/2010.181.01/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. *** java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/lopc.nc_lopc_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/lopc.nc_lopc_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/lopc.nc_lopc_pr.xml -s DConnect FileNotFound; retry open (1) http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/lopc.nc.dds DConnect FileNotFound; retry open (2) http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/lopc.nc.dds DConnect FileNotFound; retry open (3) http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/lopc.nc.dds dods.dap.DODSException: Connection cannot be opened at dods.dap.DConnect.openConnection(DConnect.java:194) at dods.dap.DConnect.getDDS(DConnect.java:273) at moos.ssds.clients.ssdsLoads.SubmitFiles.genSSDSDataContainer(Unknown Source) at moos.ssds.clients.ssdsLoads.SubmitFiles.addFiles(Unknown Source) at moos.ssds.clients.ssdsLoads.SubmitFiles.doProcessRun(Unknown Source) at moos.ssds.clients.ssdsLoads.SubmitFiles.main(Unknown Source) Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37602 updated. save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.181.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/processAUVmission_in.xml -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/processAUVmission_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/processAUVmission_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37603 updated. ************************************************************************* ************************************************************************* Processing AUV mission: 2010.181.02 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/ 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/2010/2010181/2010.181.02/navigation.nc') Creating vector time with 90237 elements. Creating vector mPos_x with 90237 elements. Creating vector time with 90237 elements. Creating vector mPos_y with 90237 elements. Creating vector time with 90237 elements. Creating vector mDepth with 90237 elements. Creating vector time with 90237 elements. Creating vector mGpsNorth with 90237 elements. Creating vector time with 90237 elements. Creating vector mGpsEast with 90237 elements. Creating vector time with 90237 elements. Creating vector mGpsValid with 90237 elements. Creating vector time with 90237 elements. Creating vector mPhi with 90237 elements. Creating vector time with 90237 elements. Creating vector mTheta with 90237 elements. Creating vector time with 90237 elements. Creating vector mPsi with 90237 elements. Creating vector time with 90237 elements. Creating vector mOmega_x with 90237 elements. Creating vector time with 90237 elements. Creating vector mOmega_y with 90237 elements. Creating vector time with 90237 elements. Creating vector mOmega_z with 90237 elements. Creating vector time with 90237 elements. Creating vector mPsaRange with 90237 elements. Creating vector time with 90237 elements. Creating vector mAltitude with 90237 elements. Creating vector time with 90237 elements. Creating vector mDvlAltitude with 90237 elements. Creating vector time with 90237 elements. Creating vector mWaterSpeed with 90237 elements. Creating vector time with 90237 elements. Creating vector mDvlValid with 90237 elements. Creating vector time with 90237 elements. Creating vector mDvlNewData with 90237 elements. Creating vector time with 90237 elements. Creating vector mDeltaT with 90237 elements. Creating vector time with 90237 elements. Creating vector nfix with 90237 elements. Creating vector time with 90237 elements. Creating vector efix with 90237 elements. Creating vector time with 90237 elements. Creating vector filter_north with 90237 elements. Creating vector time with 90237 elements. Creating vector filter_east with 90237 elements. Creating vector time with 90237 elements. Creating vector filter_depth with 90237 elements. Creating vector time with 90237 elements. Creating vector north_current with 90237 elements. Creating vector time with 90237 elements. Creating vector east_current with 90237 elements. Creating vector time with 90237 elements. Creating vector speed_bias with 90237 elements. Creating vector time with 90237 elements. Creating vector heading_bias with 90237 elements. Creating vector time with 90237 elements. Creating vector latitude with 90237 elements. Creating vector time with 90237 elements. Creating vector longitude with 90237 elements. Creating vector time with 90237 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/navigation.nc'); processNav(): median of depths = 9.6855 processNav(): Finding good depths less than 968.5527 processNav(): length(Nav.depth) = 90237 processNav(): length(gindx) = 90237 java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/navigation.nc_nav_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/navigation.nc_nav_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/navigation.nc_nav_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37604 updated. Processing GPS navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/gps.nc') Creating vector time with 1505 elements. Creating vector hours with 1505 elements. Creating vector time with 1505 elements. Creating vector minutes with 1505 elements. Creating vector time with 1505 elements. Creating vector seconds with 1505 elements. Creating vector time with 1505 elements. Creating vector centiSeconds with 1505 elements. Creating vector time with 1505 elements. Creating vector latitude with 1505 elements. Creating vector time with 1505 elements. Creating vector longitude with 1505 elements. Creating vector time with 1505 elements. Creating vector quality with 1505 elements. Creating vector time with 1505 elements. Creating vector numberOfSatellites with 1505 elements. Creating vector time with 1505 elements. Creating vector hdop with 1505 elements. Creating vector time with 1505 elements. Creating vector antennaHeight with 1505 elements. Creating vector time with 1505 elements. Creating vector geoHeight with 1505 elements. Creating vector time with 1505 elements. Creating vector dgpsDataAge with 1505 elements. Creating vector time with 1505 elements. Creating vector dgpsRSID with 1505 elements. Creating vector time with 1505 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/gps.nc'); java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/gps.nc_gps_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/gps.nc_gps_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/gps.nc_gps_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37605 updated. Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/parosci.nc') Creating vector time with 146974 elements. Creating vector depth with 146974 elements. Creating vector time with 146974 elements. Creating vector temp with 146974 elements. Creating vector time with 146974 elements. Creating vector pressure with 146974 elements. Creating vector time with 146974 elements. Creating vector temp_period with 146974 elements. Creating vector time with 146974 elements. Creating vector pres_period with 146974 elements. Creating vector time with 146974 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.18827 max(Depth.data) = 52.5174 Found 5408 bad (> 300 | < 0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = 4.7033e-06 max(Depth.data) = 52.5174 java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/parosci.nc_depth_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/parosci.nc_depth_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/parosci.nc_depth_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37606 updated. Processing hs2 backscattering and chlorophyll fluorescence data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/hydroscatlog.nc') Creating vector time with 72318 elements. Creating vector Seconds with 72318 elements. Creating vector time with 72318 elements. Creating vector HundrethsOfSeconds with 72318 elements. Creating vector time with 72318 elements. Creating vector Snorm1 with 72318 elements. Creating vector time with 72318 elements. Creating vector Snorm2 with 72318 elements. Creating vector time with 72318 elements. Creating vector Snorm3 with 72318 elements. Creating vector time with 72318 elements. Creating vector Gain_Status_1 with 72318 elements. Creating vector time with 72318 elements. Creating vector Gain_Status_2 with 72318 elements. Creating vector time with 72318 elements. Creating vector Gain_Status_3 with 72318 elements. Creating vector time with 72318 elements. Creating vector RawDepthValue with 72318 elements. Creating vector time with 72318 elements. Creating vector RawTempValue with 72318 elements. Creating vector time with 72318 elements. Creating vector Temperature with 72318 elements. Creating vector time with 72318 elements. Creating vector ErrorValue with 72318 elements. Creating vector time with 72318 elements. Creating vector bb470 with 72318 elements. Creating vector time with 72318 elements. Creating vector bb676 with 72318 elements. Creating vector time with 72318 elements. Creating vector fl676u with 72318 elements. Creating vector time with 72318 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/hydroscatlog.nc'); {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In processHS2 at 65 In processAUVmission at 128 In AUVprocess_main at 219 In reprocess_surveys at 951 java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/hydroscatlog.nc_hs2_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/hydroscatlog.nc_hs2_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/hydroscatlog.nc_hs2_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37607 updated. Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/ctdDriver.nc') Creating vector time with 72266 elements. Creating vector conductivity with 72266 elements. Creating vector time with 72266 elements. Creating vector temperature with 72266 elements. Creating vector time with 72266 elements. Creating vector cond_frequency with 72266 elements. Creating vector time with 72266 elements. Creating vector temp_frequency with 72266 elements. Creating vector time with 72266 elements. Creating vector spare with 72266 elements. Creating vector time with 72266 elements. Creating vector humidity with 72266 elements. Creating vector time with 72266 elements. Creating vector flow1 with 72266 elements. Creating vector time with 72266 elements. Creating vector rhodamine with 72266 elements. Creating vector time with 72266 elements. Creating vector dissolvedO2 with 72266 elements. Creating vector time with 72266 elements. Creating vector salinity with 72266 elements. Creating vector time with 72266 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/ctdDriver.cfg {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In processCTD at 48 In processAUVmission at 151 In AUVprocess_main at 219 In reprocess_surveys at 951 Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver.nc_ctd_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver.nc_ctd_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver.nc_ctd_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37608 updated. Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/ctdDriver2.nc') Creating vector time with 72267 elements. Creating vector conductivity with 72267 elements. Creating vector time with 72267 elements. Creating vector temperature with 72267 elements. Creating vector time with 72267 elements. Creating vector cond_frequency with 72267 elements. Creating vector time with 72267 elements. Creating vector temp_frequency with 72267 elements. Creating vector time with 72267 elements. Creating vector flow2 with 72267 elements. Creating vector time with 72267 elements. Creating vector spare with 72267 elements. Creating vector time with 72267 elements. Creating vector salinity with 72267 elements. Creating vector time with 72267 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/ctdDriver2.cfg {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In processCTD at 48 In processAUVmission at 173 In AUVprocess_main at 219 In reprocess_surveys at 951 java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver2.nc_ctd2_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver2.nc_ctd2_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ctdDriver2.nc_ctd2_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37609 updated. Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/isuslog.nc') Creating vector time with 14058 elements. Creating vector isusNitrate with 14058 elements. Creating vector time with 14058 elements. Creating vector isusTemp with 14058 elements. Creating vector time with 14058 elements. Creating vector isusQuality with 14058 elements. Creating vector time with 14058 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/isuslog.nc'); Total lag applied to nitrate = 6 seconds {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In processISUS at 22 In processAUVmission at 196 In AUVprocess_main at 219 In reprocess_surveys at 951 java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/isuslog.nc_isus_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/isuslog.nc_isus_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/isuslog.nc_isus_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37610 updated. Processing Biolume data... {Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.} > In rmpath at 58 In processBiolume at 21 In processAUVmission at 219 In AUVprocess_main at 219 In reprocess_surveys at 951 loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/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/2010/2010181/2010.181.02/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/2010/2010181/2010.181.02/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/2010/2010181/2010.181.02/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/2010/2010181/2010.181.02/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/2010/2010181/2010.181.02/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/2010/2010181/2010.181.02/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/2010/2010181/2010.181.02/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. *** java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/lopc.nc_lopc_in.txt -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/lopc.nc_lopc_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/lopc.nc_lopc_pr.xml -s DConnect FileNotFound; retry open (1) http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/lopc.nc.dds DConnect FileNotFound; retry open (2) http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/lopc.nc.dds DConnect FileNotFound; retry open (3) http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/lopc.nc.dds dods.dap.DODSException: Connection cannot be opened at dods.dap.DConnect.openConnection(DConnect.java:194) at dods.dap.DConnect.getDDS(DConnect.java:273) at moos.ssds.clients.ssdsLoads.SubmitFiles.genSSDSDataContainer(Unknown Source) at moos.ssds.clients.ssdsLoads.SubmitFiles.addFiles(Unknown Source) at moos.ssds.clients.ssdsLoads.SubmitFiles.doProcessRun(Unknown Source) at moos.ssds.clients.ssdsLoads.SubmitFiles.main(Unknown Source) Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37611 updated. save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.181.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/processAUVmission_in.xml -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/processAUVmission_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/processAUVmission_pr.xml -s Submitting metadata to SSDS (updating PR)... done. ProcessRun id = 37612 updated. ************************************************************************* ************************************************************************* Calling build_auv_survey.m to construct survey file... Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.181.01.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.181.02.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation... Looping over 12 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02.mat return Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02.mat ************************************************************************* Calling plot_sections from ../viz to produce section plots ... Using median boxcar filter of vector... Using mean boxcar filter of vector... Number of profiles found = 304 Gridding with nix = 912, iZ = 44 maskFlag = 1 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 return S O Using median boxcar filter of vector... Using median boxcar filter of vector... Using median boxcar filter of vector... bbp420 bbp700 fl700_uncorr N BL 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 gLOPC array. Masking and filtering with median filter of size 5... No valid data for gBL No valid data for gBLflow No valid data for gLOPC Encountered 0 NaN values in array of lon that is 99058 elements long ! grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath GMT_grd_is_global: no! GMT_grd_is_global: no! GMT_boundcond_param_prep determined edgeinfo: gn = 0, gs = 0, nxp = 0, nyp = 0 grdtrack: Sampled 99058 points from grid Monterey25.grd (2876 x 2447) Executing: /bin/rm -f ../results/2010181_GulperTimes.txt && touch ../results/2010181_GulperTimes.txt Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010181/2010.181.01/syslog -startEsecs 1277913390.0808 -surveyName Dorado389_2010_181_01_181_02 >> ../results/2010181_GulperTimes.txt Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2010/2010181/2010.181.02/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2010/2010181/2010.181.02/syslog -startEsecs 1277915850.1923 -surveyName Dorado389_2010_181_01_181_02 >> ../results/2010181_GulperTimes.txt Bottle: 1 Time: 1277913868.63 Depth: 13.573 Dist: 0.40292 Bottle: 2.1 Time: 1277917952.21 Depth: 7.1307 Dist: 4.2359 Bottle: 2.2 Time: 1277920086 Depth: 13.4794 Dist: 7.1139 Bottle: 2.3 Time: 1277923385.41 Depth: 8.2444 Dist: 11.1837 Bottle: 2.4 Time: 1277923408.4 Depth: 13.5642 Dist: 11.2101 Bottle: 2.5 Time: 1277928108.8 Depth: 12.8148 Dist: 17.0408 Bottle: 2.6 Time: 1277929424.4 Depth: 9.6624 Dist: 18.3856 Bottle: 2.7 Time: 1277931516.41 Depth: 10.8362 Dist: 21.2134 Bottle: 2.8 Time: 1277931525.41 Depth: 7.6366 Dist: 21.2263 Bottle: 2.9 Time: 1277931828.81 Depth: 12.6404 Dist: 21.6109 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_gridded.mat outvarstr = gF gT gN gS gD gO gB420 gB700 gBL gBLflow gLOPC idist iZ auvnav distnav ilat ilon profDist profZ dists depths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth 2Column contouring gridded variable gD Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gS Drawing bottom contour from EM300 data 2Column contouring gridded variable gN Drawing bottom contour from EM300 data 2Column contouring gridded variable gO Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_2column.png Elapsed time to save image: 4 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN Drawing bottom contour from EM300 data Biolume contouring gridded variable gO Drawing bottom contour from EM300 data Biolume contouring gridded variable gB420 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB700 Drawing bottom contour from EM300 data Biolume contouring gridded variable gF Drawing bottom contour from EM300 data Biolume contouring gridded variable gBL Drawing bottom contour from EM300 data Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_biolume.png Elapsed time to save image: 36 seconds 2Column contouring gridded variable gD Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gS Drawing bottom contour from EM300 data 2Column contouring gridded variable gN Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPC Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_lopc.png Elapsed time to save image: 4 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_2column.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_biolume.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_lopc.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2010/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ! java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/build_auv_survey_in.xml -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/build_auv_survey_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/build_auv_survey_pr.xml -s Submitting metadata to SSDS (updating PR)... done. New ProcessRun id = 37613 inserted. ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 2 NaNs found in bbpRed. Interpolating anyway. {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In interpSurvey at 128 In survey2odv at 58 In create_data_products at 325 In build_auv_survey at 485 In AUVprocess_main at 249 In reprocess_surveys at 951 1 NaNs found in flRed_uncorr. Interpolating anyway. {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In interpSurvey at 141 In survey2odv at 58 In create_data_products at 325 In build_auv_survey at 485 In AUVprocess_main at 249 In reprocess_surveys at 951 Encountered 54 NaN values in array of lon that is 15467 elements long ! grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath GMT_grd_is_global: no! GMT_grd_is_global: no! GMT_boundcond_param_prep determined edgeinfo: gn = 0, gs = 0, nxp = 0, nyp = 0 grdtrack: Sampled 15413 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 15413 are not equal to number of Lat lon points = 15467 AUV track probably goes outside of the range of the .grd file being used. Setting bottom depths to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02.txt... Copied to /mbari/AUVCTD/surveys/2010/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2010/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ! java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/build_auv_survey_out.xml -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/survey2odv_out.xml -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/survey2odv_pr.xml -s Submitting metadata to SSDS (updating PR)... done. New ProcessRun id = 37614 inserted. ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 2 NaNs found in bbpRed. Interpolating anyway. {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In interpSurvey at 128 In survey2netcdf_decim at 30 In create_data_products at 407 In build_auv_survey at 485 In AUVprocess_main at 249 In reprocess_surveys at 951 1 NaNs found in flRed_uncorr. Interpolating anyway. {Warning: NaN found in Y, interpolation at undefined values will result in undefined values.} > In interp1 at 178 In interpSurvey at 141 In survey2netcdf_decim at 30 In create_data_products at 407 In build_auv_survey at 485 In AUVprocess_main at 249 In reprocess_surveys at 951 Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_decim.nc... Copied to /mbari/AUVCTD/surveys/2010/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ! java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/build_auv_survey_out.xml -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/survey2netcdf_decim_out.txt -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/survey2netcdf_decim_pr.xml -s Submitting metadata to SSDS (updating PR)... done. New ProcessRun id = 37615 inserted. ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02.nc... Copied to /mbari/AUVCTD/surveys/2010/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ! java -jar ssdsLoads-new-ssds.jar -i /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/build_auv_survey_out.xml -o /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/survey2netcdf_out.txt -u /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/survey2netcdf_pr.xml -s Submitting metadata to SSDS (updating PR)... done. New ProcessRun id = 37616 inserted. Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02_gridded.mat... Copied to /mbari/AUVCTD/surveys/2010/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010_181_01_181_02.mat... Copied to /mbari/AUVCTD/surveys/2010/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2010_181_01_181_02 processed" mccann@mbari.org < mail_Dorado389_2010_181_01_181_02.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.181.01.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2010.181.02.mat Processing time: 33 seconds