Execution of AUVprocess_main version 1.86 at 2018-06-01T22:03:38Z on elvis Matlab command executed: AUVprocess_main('OCCO', 2004, ['345.01';'345.02';'345.03';'345.04';'345.05';'345.06';'345.07';'345.08'], '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: 2004.345.01 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/ 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/2004/2004345/2004.345.01/navigation.nc') Creating vector time with 8731 elements. Creating vector mPos_x with 8731 elements. Creating vector time with 8731 elements. Creating vector mPos_y with 8731 elements. Creating vector time with 8731 elements. Creating vector mDepth with 8731 elements. Creating vector time with 8731 elements. Creating vector mGpsNorth with 8731 elements. Creating vector time with 8731 elements. Creating vector mGpsEast with 8731 elements. Creating vector time with 8731 elements. Creating vector mGpsValid with 8731 elements. Creating vector time with 8731 elements. Creating vector mPhi with 8731 elements. Creating vector time with 8731 elements. Creating vector mTheta with 8731 elements. Creating vector time with 8731 elements. Creating vector mPsi with 8731 elements. Creating vector time with 8731 elements. Creating vector mOmega_x with 8731 elements. Creating vector time with 8731 elements. Creating vector mOmega_y with 8731 elements. Creating vector time with 8731 elements. Creating vector mOmega_z with 8731 elements. Creating vector time with 8731 elements. Creating vector mPsaRange with 8731 elements. Creating vector time with 8731 elements. Creating vector mAltitude with 8731 elements. Creating vector time with 8731 elements. Creating vector mWaterSpeed with 8731 elements. Creating vector time with 8731 elements. Creating vector mDvlValid with 8731 elements. Creating vector time with 8731 elements. Creating vector mDvlNewData with 8731 elements. Creating vector time with 8731 elements. Creating vector mDeltaT with 8731 elements. Creating vector time with 8731 elements. Creating vector latitude with 8731 elements. Creating vector time with 8731 elements. Creating vector longitude with 8731 elements. Creating vector time with 8731 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/navigation.nc'); processNav(): median of positive valued depths = 9.0037 processNav(): Finding depths less than 63.0257 and times > 0 processNav(): length(Nav.depth) = 8731 processNav(): length(gindx) = 8731 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/2004/2004345/2004.345.01/gps.nc') Creating vector time with 394 elements. Creating vector hours with 394 elements. Creating vector time with 394 elements. Creating vector minutes with 394 elements. Creating vector time with 394 elements. Creating vector seconds with 394 elements. Creating vector time with 394 elements. Creating vector centiSeconds with 394 elements. Creating vector time with 394 elements. Creating vector latitude with 394 elements. Creating vector time with 394 elements. Creating vector longitude with 394 elements. Creating vector time with 394 elements. Creating vector quality with 394 elements. Creating vector time with 394 elements. Creating vector numberOfSatellites with 394 elements. Creating vector time with 394 elements. Creating vector hdop with 394 elements. Creating vector time with 394 elements. Creating vector antennaHeight with 394 elements. Creating vector time with 394 elements. Creating vector geoHeight with 394 elements. Creating vector time with 394 elements. Creating vector dgpsDataAge with 394 elements. Creating vector time with 394 elements. Creating vector dgpsRSID with 394 elements. Creating vector time with 394 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/parosci.nc') Creating vector time with 8836 elements. Creating vector depth with 8836 elements. Creating vector time with 8836 elements. Creating vector temp with 8836 elements. Creating vector time with 8836 elements. Creating vector pressure with 8836 elements. Creating vector time with 8836 elements. Creating vector temp_period with 8836 elements. Creating vector time with 8836 elements. Creating vector pres_period with 8836 elements. Creating vector time with 8836 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.22149 max(Depth.data) = 16.0998 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.22149 max(Depth.data) = 16.0998 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/2004/2004345/2004.345.01/hydroscatlog.nc') Creating vector time with 7051 elements. Creating vector Seconds with 7051 elements. Creating vector time with 7051 elements. Creating vector HundrethsOfSeconds with 7051 elements. Creating vector time with 7051 elements. Creating vector Snorm1 with 7051 elements. Creating vector time with 7051 elements. Creating vector Snorm2 with 7051 elements. Creating vector time with 7051 elements. Creating vector Snorm3 with 7051 elements. Creating vector time with 7051 elements. Creating vector Gain_Status_1 with 7051 elements. Creating vector time with 7051 elements. Creating vector Gain_Status_2 with 7051 elements. Creating vector time with 7051 elements. Creating vector Gain_Status_3 with 7051 elements. Creating vector time with 7051 elements. Creating vector RawDepthValue with 7051 elements. Creating vector time with 7051 elements. Creating vector RawTempValue with 7051 elements. Creating vector time with 7051 elements. Creating vector Temperature with 7051 elements. Creating vector time with 7051 elements. Creating vector ErrorValue with 7051 elements. Creating vector time with 7051 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/ctdDriver.nc') Creating vector time with 6963 elements. Creating vector conductivity with 6963 elements. Creating vector time with 6963 elements. Creating vector temperature with 6963 elements. Creating vector time with 6963 elements. Creating vector cond_frequency with 6963 elements. Creating vector time with 6963 elements. Creating vector temp_frequency with 6963 elements. Creating vector time with 6963 elements. Creating vector spare with 6963 elements. Creating vector time with 6963 elements. Creating vector humidity with 6963 elements. Creating vector time with 6963 elements. Creating vector flow1 with 6963 elements. Creating vector time with 6963 elements. Creating vector OBS with 6963 elements. Creating vector time with 6963 elements. Creating vector dissolvedO2 with 6963 elements. Creating vector time with 6963 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/ctdDriver2.nc') Creating vector time with 6893 elements. Creating vector conductivity with 6893 elements. Creating vector time with 6893 elements. Creating vector temperature with 6893 elements. Creating vector time with 6893 elements. Creating vector cond_frequency with 6893 elements. Creating vector time with 6893 elements. Creating vector temp_frequency with 6893 elements. Creating vector time with 6893 elements. Creating vector flow2 with 6893 elements. Creating vector time with 6893 elements. Creating vector spare with 6893 elements. Creating vector time with 6893 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/isuslog.nc') Creating vector time with 1112 elements. Creating vector isusNitrate with 1112 elements. Creating vector time with 1112 elements. Creating vector isusTemp with 1112 elements. Creating vector time with 1112 elements. Creating vector isusQuality with 1112 elements. Creating vector time with 1112 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.01/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/2004/2004345/2004.345.01/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/2004/2004345/2004.345.01/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/2004/2004345/2004.345.01/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/2004/2004345/2004.345.01/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/2004/2004345/2004.345.01/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/2004/2004345/2004.345.01/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/2004/2004345/2004.345.01/lopc.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.01.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2004.345.02 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/ 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/2004/2004345/2004.345.02/navigation.nc') Creating vector time with 4571 elements. Creating vector mPos_x with 4571 elements. Creating vector time with 4571 elements. Creating vector mPos_y with 4571 elements. Creating vector time with 4571 elements. Creating vector mDepth with 4571 elements. Creating vector time with 4571 elements. Creating vector mGpsNorth with 4571 elements. Creating vector time with 4571 elements. Creating vector mGpsEast with 4571 elements. Creating vector time with 4571 elements. Creating vector mGpsValid with 4571 elements. Creating vector time with 4571 elements. Creating vector mPhi with 4571 elements. Creating vector time with 4571 elements. Creating vector mTheta with 4571 elements. Creating vector time with 4571 elements. Creating vector mPsi with 4571 elements. Creating vector time with 4571 elements. Creating vector mOmega_x with 4571 elements. Creating vector time with 4571 elements. Creating vector mOmega_y with 4571 elements. Creating vector time with 4571 elements. Creating vector mOmega_z with 4571 elements. Creating vector time with 4571 elements. Creating vector mPsaRange with 4571 elements. Creating vector time with 4571 elements. Creating vector mAltitude with 4571 elements. Creating vector time with 4571 elements. Creating vector mWaterSpeed with 4571 elements. Creating vector time with 4571 elements. Creating vector mDvlValid with 4571 elements. Creating vector time with 4571 elements. Creating vector mDvlNewData with 4571 elements. Creating vector time with 4571 elements. Creating vector mDeltaT with 4571 elements. Creating vector time with 4571 elements. Creating vector latitude with 4571 elements. Creating vector time with 4571 elements. Creating vector longitude with 4571 elements. Creating vector time with 4571 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/navigation.nc'); processNav(): median of positive valued depths = 7.6676 processNav(): Finding depths less than 53.6729 and times > 0 processNav(): length(Nav.depth) = 4571 processNav(): length(gindx) = 4571 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/2004/2004345/2004.345.02/gps.nc') Creating vector time with 119 elements. Creating vector hours with 119 elements. Creating vector time with 119 elements. Creating vector minutes with 119 elements. Creating vector time with 119 elements. Creating vector seconds with 119 elements. Creating vector time with 119 elements. Creating vector centiSeconds with 119 elements. Creating vector time with 119 elements. Creating vector latitude with 119 elements. Creating vector time with 119 elements. Creating vector longitude with 119 elements. Creating vector time with 119 elements. Creating vector quality with 119 elements. Creating vector time with 119 elements. Creating vector numberOfSatellites with 119 elements. Creating vector time with 119 elements. Creating vector hdop with 119 elements. Creating vector time with 119 elements. Creating vector antennaHeight with 119 elements. Creating vector time with 119 elements. Creating vector geoHeight with 119 elements. Creating vector time with 119 elements. Creating vector dgpsDataAge with 119 elements. Creating vector time with 119 elements. Creating vector dgpsRSID with 119 elements. Creating vector time with 119 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/parosci.nc') Creating vector time with 4674 elements. Creating vector depth with 4674 elements. Creating vector time with 4674 elements. Creating vector temp with 4674 elements. Creating vector time with 4674 elements. Creating vector pressure with 4674 elements. Creating vector time with 4674 elements. Creating vector temp_period with 4674 elements. Creating vector time with 4674 elements. Creating vector pres_period with 4674 elements. Creating vector time with 4674 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.14164 max(Depth.data) = 14.4839 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.14164 max(Depth.data) = 14.4839 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/2004/2004345/2004.345.02/hydroscatlog.nc') Creating vector time with 3725 elements. Creating vector Seconds with 3725 elements. Creating vector time with 3725 elements. Creating vector HundrethsOfSeconds with 3725 elements. Creating vector time with 3725 elements. Creating vector Snorm1 with 3725 elements. Creating vector time with 3725 elements. Creating vector Snorm2 with 3725 elements. Creating vector time with 3725 elements. Creating vector Snorm3 with 3725 elements. Creating vector time with 3725 elements. Creating vector Gain_Status_1 with 3725 elements. Creating vector time with 3725 elements. Creating vector Gain_Status_2 with 3725 elements. Creating vector time with 3725 elements. Creating vector Gain_Status_3 with 3725 elements. Creating vector time with 3725 elements. Creating vector RawDepthValue with 3725 elements. Creating vector time with 3725 elements. Creating vector RawTempValue with 3725 elements. Creating vector time with 3725 elements. Creating vector Temperature with 3725 elements. Creating vector time with 3725 elements. Creating vector ErrorValue with 3725 elements. Creating vector time with 3725 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/ctdDriver.nc') Creating vector time with 3668 elements. Creating vector conductivity with 3668 elements. Creating vector time with 3668 elements. Creating vector temperature with 3668 elements. Creating vector time with 3668 elements. Creating vector cond_frequency with 3668 elements. Creating vector time with 3668 elements. Creating vector temp_frequency with 3668 elements. Creating vector time with 3668 elements. Creating vector spare with 3668 elements. Creating vector time with 3668 elements. Creating vector humidity with 3668 elements. Creating vector time with 3668 elements. Creating vector flow1 with 3668 elements. Creating vector time with 3668 elements. Creating vector OBS with 3668 elements. Creating vector time with 3668 elements. Creating vector dissolvedO2 with 3668 elements. Creating vector time with 3668 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/ctdDriver2.nc') Creating vector time with 3693 elements. Creating vector conductivity with 3693 elements. Creating vector time with 3693 elements. Creating vector temperature with 3693 elements. Creating vector time with 3693 elements. Creating vector cond_frequency with 3693 elements. Creating vector time with 3693 elements. Creating vector temp_frequency with 3693 elements. Creating vector time with 3693 elements. Creating vector flow2 with 3693 elements. Creating vector time with 3693 elements. Creating vector spare with 3693 elements. Creating vector time with 3693 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/isuslog.nc') Creating vector time with 556 elements. Creating vector isusNitrate with 556 elements. Creating vector time with 556 elements. Creating vector isusTemp with 556 elements. Creating vector time with 556 elements. Creating vector isusQuality with 556 elements. Creating vector time with 556 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.02/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/2004/2004345/2004.345.02/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/2004/2004345/2004.345.02/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/2004/2004345/2004.345.02/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/2004/2004345/2004.345.02/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/2004/2004345/2004.345.02/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/2004/2004345/2004.345.02/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/2004/2004345/2004.345.02/lopc.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.02.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2004.345.03 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.03/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.03/ 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/2004/2004345/2004.345.03/navigation.nc') Creating vector time with 74324 elements. Creating vector mPos_x with 74324 elements. Creating vector time with 74324 elements. Creating vector mPos_y with 74324 elements. Creating vector time with 74324 elements. Creating vector mDepth with 74324 elements. Creating vector time with 74324 elements. Creating vector mGpsNorth with 74324 elements. Creating vector time with 74324 elements. Creating vector mGpsEast with 74324 elements. Creating vector time with 74324 elements. Creating vector mGpsValid with 74324 elements. Creating vector time with 74324 elements. Creating vector mPhi with 74324 elements. Creating vector time with 74324 elements. Creating vector mTheta with 74324 elements. Creating vector time with 74324 elements. Creating vector mPsi with 74324 elements. Creating vector time with 74324 elements. Creating vector mOmega_x with 74324 elements. Creating vector time with 74324 elements. Creating vector mOmega_y with 74324 elements. Creating vector time with 74324 elements. Creating vector mOmega_z with 74324 elements. Creating vector time with 74324 elements. Creating vector mPsaRange with 74324 elements. Creating vector time with 74324 elements. Creating vector mAltitude with 74324 elements. Creating vector time with 74324 elements. Creating vector mWaterSpeed with 74324 elements. Creating vector time with 74324 elements. Creating vector mDvlValid with 74324 elements. Creating vector time with 74324 elements. Creating vector mDvlNewData with 74324 elements. Creating vector time with 74324 elements. Creating vector mDeltaT with 74324 elements. Creating vector time with 74324 elements. Creating vector latitude with 74324 elements. Creating vector time with 74324 elements. Creating vector longitude with 74324 elements. Creating vector time with 74324 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.03/navigation.nc'); processNav(): median of positive valued depths = 8.015 processNav(): Finding depths less than 56.1049 and times > 0 processNav(): length(Nav.depth) = 74324 processNav(): length(gindx) = 74324 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/2004/2004345/2004.345.03/gps.nc') Creating vector time with 711 elements. Creating vector hours with 711 elements. Creating vector time with 711 elements. Creating vector minutes with 711 elements. Creating vector time with 711 elements. Creating vector seconds with 711 elements. Creating vector time with 711 elements. Creating vector centiSeconds with 711 elements. Creating vector time with 711 elements. Creating vector latitude with 711 elements. Creating vector time with 711 elements. Creating vector longitude with 711 elements. Creating vector time with 711 elements. Creating vector quality with 711 elements. Creating vector time with 711 elements. Creating vector numberOfSatellites with 711 elements. Creating vector time with 711 elements. Creating vector hdop with 711 elements. Creating vector time with 711 elements. Creating vector antennaHeight with 711 elements. Creating vector time with 711 elements. Creating vector geoHeight with 711 elements. Creating vector time with 711 elements. Creating vector dgpsDataAge with 711 elements. Creating vector time with 711 elements. Creating vector dgpsRSID with 711 elements. Creating vector time with 711 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/parosci.nc') Creating vector time with 74431 elements. Creating vector depth with 74431 elements. Creating vector time with 74431 elements. Creating vector temp with 74431 elements. Creating vector time with 74431 elements. Creating vector pressure with 74431 elements. Creating vector time with 74431 elements. Creating vector temp_period with 74431 elements. Creating vector time with 74431 elements. Creating vector pres_period with 74431 elements. Creating vector time with 74431 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.03/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.19989 max(Depth.data) = 16.8745 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.19989 max(Depth.data) = 16.8745 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/2004/2004345/2004.345.03/hydroscatlog.nc') Creating vector time with 59505 elements. Creating vector Seconds with 59505 elements. Creating vector time with 59505 elements. Creating vector HundrethsOfSeconds with 59505 elements. Creating vector time with 59505 elements. Creating vector Snorm1 with 59505 elements. Creating vector time with 59505 elements. Creating vector Snorm2 with 59505 elements. Creating vector time with 59505 elements. Creating vector Snorm3 with 59505 elements. Creating vector time with 59505 elements. Creating vector Gain_Status_1 with 59505 elements. Creating vector time with 59505 elements. Creating vector Gain_Status_2 with 59505 elements. Creating vector time with 59505 elements. Creating vector Gain_Status_3 with 59505 elements. Creating vector time with 59505 elements. Creating vector RawDepthValue with 59505 elements. Creating vector time with 59505 elements. Creating vector RawTempValue with 59505 elements. Creating vector time with 59505 elements. Creating vector Temperature with 59505 elements. Creating vector time with 59505 elements. Creating vector ErrorValue with 59505 elements. Creating vector time with 59505 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/ctdDriver.nc') Creating vector time with 59435 elements. Creating vector conductivity with 59435 elements. Creating vector time with 59435 elements. Creating vector temperature with 59435 elements. Creating vector time with 59435 elements. Creating vector cond_frequency with 59435 elements. Creating vector time with 59435 elements. Creating vector temp_frequency with 59435 elements. Creating vector time with 59435 elements. Creating vector spare with 59435 elements. Creating vector time with 59435 elements. Creating vector humidity with 59435 elements. Creating vector time with 59435 elements. Creating vector flow1 with 59435 elements. Creating vector time with 59435 elements. Creating vector OBS with 59435 elements. Creating vector time with 59435 elements. Creating vector dissolvedO2 with 59435 elements. Creating vector time with 59435 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.03/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/ctdDriver2.nc') Creating vector time with 58784 elements. Creating vector conductivity with 58784 elements. Creating vector time with 58784 elements. Creating vector temperature with 58784 elements. Creating vector time with 58784 elements. Creating vector cond_frequency with 58784 elements. Creating vector time with 58784 elements. Creating vector temp_frequency with 58784 elements. Creating vector time with 58784 elements. Creating vector flow2 with 58784 elements. Creating vector time with 58784 elements. Creating vector spare with 58784 elements. Creating vector time with 58784 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.03/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/isuslog.nc') Creating vector time with 9588 elements. Creating vector isusNitrate with 9588 elements. Creating vector time with 9588 elements. Creating vector isusTemp with 9588 elements. Creating vector time with 9588 elements. Creating vector isusQuality with 9588 elements. Creating vector time with 9588 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/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/2004/2004345/2004.345.03/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_2004.345.03.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2004.345.04 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/navigation.nc') Creating vector time with 1060 elements. Creating vector mPos_x with 1060 elements. Creating vector time with 1060 elements. Creating vector mPos_y with 1060 elements. Creating vector time with 1060 elements. Creating vector mDepth with 1060 elements. Creating vector time with 1060 elements. Creating vector mGpsNorth with 1060 elements. Creating vector time with 1060 elements. Creating vector mGpsEast with 1060 elements. Creating vector time with 1060 elements. Creating vector mGpsValid with 1060 elements. Creating vector time with 1060 elements. Creating vector mPhi with 1060 elements. Creating vector time with 1060 elements. Creating vector mTheta with 1060 elements. Creating vector time with 1060 elements. Creating vector mPsi with 1060 elements. Creating vector time with 1060 elements. Creating vector mOmega_x with 1060 elements. Creating vector time with 1060 elements. Creating vector mOmega_y with 1060 elements. Creating vector time with 1060 elements. Creating vector mOmega_z with 1060 elements. Creating vector time with 1060 elements. Creating vector mPsaRange with 1060 elements. Creating vector time with 1060 elements. Creating vector mAltitude with 1060 elements. Creating vector time with 1060 elements. Creating vector mWaterSpeed with 1060 elements. Creating vector time with 1060 elements. Creating vector mDvlValid with 1060 elements. Creating vector time with 1060 elements. Creating vector mDvlNewData with 1060 elements. Creating vector time with 1060 elements. Creating vector mDeltaT with 1060 elements. Creating vector time with 1060 elements. Creating vector latitude with 1060 elements. Creating vector time with 1060 elements. Creating vector longitude with 1060 elements. Creating vector time with 1060 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/navigation.nc'); processNav(): median of positive valued depths = 3.5571 processNav(): Finding depths less than 24.8994 and times > 0 processNav(): length(Nav.depth) = 1060 processNav(): length(gindx) = 1060 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/2004/2004345/2004.345.04/gps.nc') Creating vector time with 154 elements. Creating vector hours with 154 elements. Creating vector time with 154 elements. Creating vector minutes with 154 elements. Creating vector time with 154 elements. Creating vector seconds with 154 elements. Creating vector time with 154 elements. Creating vector centiSeconds with 154 elements. Creating vector time with 154 elements. Creating vector latitude with 154 elements. Creating vector time with 154 elements. Creating vector longitude with 154 elements. Creating vector time with 154 elements. Creating vector quality with 154 elements. Creating vector time with 154 elements. Creating vector numberOfSatellites with 154 elements. Creating vector time with 154 elements. Creating vector hdop with 154 elements. Creating vector time with 154 elements. Creating vector antennaHeight with 154 elements. Creating vector time with 154 elements. Creating vector geoHeight with 154 elements. Creating vector time with 154 elements. Creating vector dgpsDataAge with 154 elements. Creating vector time with 154 elements. Creating vector dgpsRSID with 154 elements. Creating vector time with 154 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/parosci.nc') Creating vector time with 1166 elements. Creating vector depth with 1166 elements. Creating vector time with 1166 elements. Creating vector temp with 1166 elements. Creating vector time with 1166 elements. Creating vector pressure with 1166 elements. Creating vector time with 1166 elements. Creating vector temp_period with 1166 elements. Creating vector time with 1166 elements. Creating vector pres_period with 1166 elements. Creating vector time with 1166 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.12445 max(Depth.data) = 9.3197 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.12445 max(Depth.data) = 9.3197 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/2004/2004345/2004.345.04/hydroscatlog.nc') Creating vector time with 917 elements. Creating vector Seconds with 917 elements. Creating vector time with 917 elements. Creating vector HundrethsOfSeconds with 917 elements. Creating vector time with 917 elements. Creating vector Snorm1 with 917 elements. Creating vector time with 917 elements. Creating vector Snorm2 with 917 elements. Creating vector time with 917 elements. Creating vector Snorm3 with 917 elements. Creating vector time with 917 elements. Creating vector Gain_Status_1 with 917 elements. Creating vector time with 917 elements. Creating vector Gain_Status_2 with 917 elements. Creating vector time with 917 elements. Creating vector Gain_Status_3 with 917 elements. Creating vector time with 917 elements. Creating vector RawDepthValue with 917 elements. Creating vector time with 917 elements. Creating vector RawTempValue with 917 elements. Creating vector time with 917 elements. Creating vector Temperature with 917 elements. Creating vector time with 917 elements. Creating vector ErrorValue with 917 elements. Creating vector time with 917 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/ctdDriver.nc') Creating vector time with 858 elements. Creating vector conductivity with 858 elements. Creating vector time with 858 elements. Creating vector temperature with 858 elements. Creating vector time with 858 elements. Creating vector cond_frequency with 858 elements. Creating vector time with 858 elements. Creating vector temp_frequency with 858 elements. Creating vector time with 858 elements. Creating vector spare with 858 elements. Creating vector time with 858 elements. Creating vector humidity with 858 elements. Creating vector time with 858 elements. Creating vector flow1 with 858 elements. Creating vector time with 858 elements. Creating vector OBS with 858 elements. Creating vector time with 858 elements. Creating vector dissolvedO2 with 858 elements. Creating vector time with 858 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/ctdDriver2.nc') Creating vector time with 885 elements. Creating vector conductivity with 885 elements. Creating vector time with 885 elements. Creating vector temperature with 885 elements. Creating vector time with 885 elements. Creating vector cond_frequency with 885 elements. Creating vector time with 885 elements. Creating vector temp_frequency with 885 elements. Creating vector time with 885 elements. Creating vector flow2 with 885 elements. Creating vector time with 885 elements. Creating vector spare with 885 elements. Creating vector time with 885 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/isuslog.nc') Creating vector time with 101 elements. Creating vector isusNitrate with 101 elements. Creating vector time with 101 elements. Creating vector isusTemp with 101 elements. Creating vector time with 101 elements. Creating vector isusQuality with 101 elements. Creating vector time with 101 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/biolume.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/biolume.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/biolume.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/biolume.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. Could not read from biolume.nc returning NaNs for fields. Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/lopc.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/lopc.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/lopc.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.04/lopc.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.04.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2004.345.05 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.05/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.05/ 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/2004/2004345/2004.345.05/navigation.nc') Creating vector time with 19513 elements. Creating vector mPos_x with 19513 elements. Creating vector time with 19513 elements. Creating vector mPos_y with 19513 elements. Creating vector time with 19513 elements. Creating vector mDepth with 19513 elements. Creating vector time with 19513 elements. Creating vector mGpsNorth with 19513 elements. Creating vector time with 19513 elements. Creating vector mGpsEast with 19513 elements. Creating vector time with 19513 elements. Creating vector mGpsValid with 19513 elements. Creating vector time with 19513 elements. Creating vector mPhi with 19513 elements. Creating vector time with 19513 elements. Creating vector mTheta with 19513 elements. Creating vector time with 19513 elements. Creating vector mPsi with 19513 elements. Creating vector time with 19513 elements. Creating vector mOmega_x with 19513 elements. Creating vector time with 19513 elements. Creating vector mOmega_y with 19513 elements. Creating vector time with 19513 elements. Creating vector mOmega_z with 19513 elements. Creating vector time with 19513 elements. Creating vector mPsaRange with 19513 elements. Creating vector time with 19513 elements. Creating vector mAltitude with 19513 elements. Creating vector time with 19513 elements. Creating vector mWaterSpeed with 19513 elements. Creating vector time with 19513 elements. Creating vector mDvlValid with 19513 elements. Creating vector time with 19513 elements. Creating vector mDvlNewData with 19513 elements. Creating vector time with 19513 elements. Creating vector mDeltaT with 19513 elements. Creating vector time with 19513 elements. Creating vector latitude with 19513 elements. Creating vector time with 19513 elements. Creating vector longitude with 19513 elements. Creating vector time with 19513 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.05/navigation.nc'); processNav(): median of positive valued depths = 7.7435 processNav(): Finding depths less than 54.2043 and times > 0 processNav(): length(Nav.depth) = 19513 processNav(): length(gindx) = 19513 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/2004/2004345/2004.345.05/gps.nc') Creating vector time with 276 elements. Creating vector hours with 276 elements. Creating vector time with 276 elements. Creating vector minutes with 276 elements. Creating vector time with 276 elements. Creating vector seconds with 276 elements. Creating vector time with 276 elements. Creating vector centiSeconds with 276 elements. Creating vector time with 276 elements. Creating vector latitude with 276 elements. Creating vector time with 276 elements. Creating vector longitude with 276 elements. Creating vector time with 276 elements. Creating vector quality with 276 elements. Creating vector time with 276 elements. Creating vector numberOfSatellites with 276 elements. Creating vector time with 276 elements. Creating vector hdop with 276 elements. Creating vector time with 276 elements. Creating vector antennaHeight with 276 elements. Creating vector time with 276 elements. Creating vector geoHeight with 276 elements. Creating vector time with 276 elements. Creating vector dgpsDataAge with 276 elements. Creating vector time with 276 elements. Creating vector dgpsRSID with 276 elements. Creating vector time with 276 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/parosci.nc') Creating vector time with 19618 elements. Creating vector depth with 19618 elements. Creating vector time with 19618 elements. Creating vector temp with 19618 elements. Creating vector time with 19618 elements. Creating vector pressure with 19618 elements. Creating vector time with 19618 elements. Creating vector temp_period with 19618 elements. Creating vector time with 19618 elements. Creating vector pres_period with 19618 elements. Creating vector time with 19618 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.05/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.068796 max(Depth.data) = 15.8917 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.068796 max(Depth.data) = 15.8917 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/2004/2004345/2004.345.05/hydroscatlog.nc') Creating vector time with 15673 elements. Creating vector Seconds with 15673 elements. Creating vector time with 15673 elements. Creating vector HundrethsOfSeconds with 15673 elements. Creating vector time with 15673 elements. Creating vector Snorm1 with 15673 elements. Creating vector time with 15673 elements. Creating vector Snorm2 with 15673 elements. Creating vector time with 15673 elements. Creating vector Snorm3 with 15673 elements. Creating vector time with 15673 elements. Creating vector Gain_Status_1 with 15673 elements. Creating vector time with 15673 elements. Creating vector Gain_Status_2 with 15673 elements. Creating vector time with 15673 elements. Creating vector Gain_Status_3 with 15673 elements. Creating vector time with 15673 elements. Creating vector RawDepthValue with 15673 elements. Creating vector time with 15673 elements. Creating vector RawTempValue with 15673 elements. Creating vector time with 15673 elements. Creating vector Temperature with 15673 elements. Creating vector time with 15673 elements. Creating vector ErrorValue with 15673 elements. Creating vector time with 15673 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/ctdDriver.nc') Creating vector time with 15623 elements. Creating vector conductivity with 15623 elements. Creating vector time with 15623 elements. Creating vector temperature with 15623 elements. Creating vector time with 15623 elements. Creating vector cond_frequency with 15623 elements. Creating vector time with 15623 elements. Creating vector temp_frequency with 15623 elements. Creating vector time with 15623 elements. Creating vector spare with 15623 elements. Creating vector time with 15623 elements. Creating vector humidity with 15623 elements. Creating vector time with 15623 elements. Creating vector flow1 with 15623 elements. Creating vector time with 15623 elements. Creating vector OBS with 15623 elements. Creating vector time with 15623 elements. Creating vector dissolvedO2 with 15623 elements. Creating vector time with 15623 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.05/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/ctdDriver2.nc') Creating vector time with 15644 elements. Creating vector conductivity with 15644 elements. Creating vector time with 15644 elements. Creating vector temperature with 15644 elements. Creating vector time with 15644 elements. Creating vector cond_frequency with 15644 elements. Creating vector time with 15644 elements. Creating vector temp_frequency with 15644 elements. Creating vector time with 15644 elements. Creating vector flow2 with 15644 elements. Creating vector time with 15644 elements. Creating vector spare with 15644 elements. Creating vector time with 15644 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.05/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/isuslog.nc') Creating vector time with 2491 elements. Creating vector isusNitrate with 2491 elements. Creating vector time with 2491 elements. Creating vector isusTemp with 2491 elements. Creating vector time with 2491 elements. Creating vector isusQuality with 2491 elements. Creating vector time with 2491 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/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/2004/2004345/2004.345.05/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_2004.345.05.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2004.345.06 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.06/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.06/ 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/2004/2004345/2004.345.06/navigation.nc') Creating vector time with 894 elements. Creating vector mPos_x with 894 elements. Creating vector time with 894 elements. Creating vector mPos_y with 894 elements. Creating vector time with 894 elements. Creating vector mDepth with 894 elements. Creating vector time with 894 elements. Creating vector mGpsNorth with 894 elements. Creating vector time with 894 elements. Creating vector mGpsEast with 894 elements. Creating vector time with 894 elements. Creating vector mGpsValid with 894 elements. Creating vector time with 894 elements. Creating vector mPhi with 894 elements. Creating vector time with 894 elements. Creating vector mTheta with 894 elements. Creating vector time with 894 elements. Creating vector mPsi with 894 elements. Creating vector time with 894 elements. Creating vector mOmega_x with 894 elements. Creating vector time with 894 elements. Creating vector mOmega_y with 894 elements. Creating vector time with 894 elements. Creating vector mOmega_z with 894 elements. Creating vector time with 894 elements. Creating vector mPsaRange with 894 elements. Creating vector time with 894 elements. Creating vector mAltitude with 894 elements. Creating vector time with 894 elements. Creating vector mWaterSpeed with 894 elements. Creating vector time with 894 elements. Creating vector mDvlValid with 894 elements. Creating vector time with 894 elements. Creating vector mDvlNewData with 894 elements. Creating vector time with 894 elements. Creating vector mDeltaT with 894 elements. Creating vector time with 894 elements. Creating vector latitude with 894 elements. Creating vector time with 894 elements. Creating vector longitude with 894 elements. Creating vector time with 894 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.06/navigation.nc'); processNav(): median of positive valued depths = 2.7545 processNav(): Finding depths less than 19.2817 and times > 0 processNav(): length(Nav.depth) = 894 processNav(): length(gindx) = 894 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/2004/2004345/2004.345.06/gps.nc') Creating vector time with 125 elements. Creating vector hours with 125 elements. Creating vector time with 125 elements. Creating vector minutes with 125 elements. Creating vector time with 125 elements. Creating vector seconds with 125 elements. Creating vector time with 125 elements. Creating vector centiSeconds with 125 elements. Creating vector time with 125 elements. Creating vector latitude with 125 elements. Creating vector time with 125 elements. Creating vector longitude with 125 elements. Creating vector time with 125 elements. Creating vector quality with 125 elements. Creating vector time with 125 elements. Creating vector numberOfSatellites with 125 elements. Creating vector time with 125 elements. Creating vector hdop with 125 elements. Creating vector time with 125 elements. Creating vector antennaHeight with 125 elements. Creating vector time with 125 elements. Creating vector geoHeight with 125 elements. Creating vector time with 125 elements. Creating vector dgpsDataAge with 125 elements. Creating vector time with 125 elements. Creating vector dgpsRSID with 125 elements. Creating vector time with 125 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/parosci.nc') Creating vector time with 995 elements. Creating vector depth with 995 elements. Creating vector time with 995 elements. Creating vector temp with 995 elements. Creating vector time with 995 elements. Creating vector pressure with 995 elements. Creating vector time with 995 elements. Creating vector temp_period with 995 elements. Creating vector time with 995 elements. Creating vector pres_period with 995 elements. Creating vector time with 995 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.06/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.22029 max(Depth.data) = 8.6109 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.22029 max(Depth.data) = 8.6109 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/2004/2004345/2004.345.06/hydroscatlog.nc') Creating vector time with 778 elements. Creating vector Seconds with 778 elements. Creating vector time with 778 elements. Creating vector HundrethsOfSeconds with 778 elements. Creating vector time with 778 elements. Creating vector Snorm1 with 778 elements. Creating vector time with 778 elements. Creating vector Snorm2 with 778 elements. Creating vector time with 778 elements. Creating vector Snorm3 with 778 elements. Creating vector time with 778 elements. Creating vector Gain_Status_1 with 778 elements. Creating vector time with 778 elements. Creating vector Gain_Status_2 with 778 elements. Creating vector time with 778 elements. Creating vector Gain_Status_3 with 778 elements. Creating vector time with 778 elements. Creating vector RawDepthValue with 778 elements. Creating vector time with 778 elements. Creating vector RawTempValue with 778 elements. Creating vector time with 778 elements. Creating vector Temperature with 778 elements. Creating vector time with 778 elements. Creating vector ErrorValue with 778 elements. Creating vector time with 778 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/ctdDriver.nc') Creating vector time with 721 elements. Creating vector conductivity with 721 elements. Creating vector time with 721 elements. Creating vector temperature with 721 elements. Creating vector time with 721 elements. Creating vector cond_frequency with 721 elements. Creating vector time with 721 elements. Creating vector temp_frequency with 721 elements. Creating vector time with 721 elements. Creating vector spare with 721 elements. Creating vector time with 721 elements. Creating vector humidity with 721 elements. Creating vector time with 721 elements. Creating vector flow1 with 721 elements. Creating vector time with 721 elements. Creating vector OBS with 721 elements. Creating vector time with 721 elements. Creating vector dissolvedO2 with 721 elements. Creating vector time with 721 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.06/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/ctdDriver2.nc') Creating vector time with 749 elements. Creating vector conductivity with 749 elements. Creating vector time with 749 elements. Creating vector temperature with 749 elements. Creating vector time with 749 elements. Creating vector cond_frequency with 749 elements. Creating vector time with 749 elements. Creating vector temp_frequency with 749 elements. Creating vector time with 749 elements. Creating vector flow2 with 749 elements. Creating vector time with 749 elements. Creating vector spare with 749 elements. Creating vector time with 749 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.06/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/isuslog.nc') Creating vector time with 80 elements. Creating vector isusNitrate with 80 elements. Creating vector time with 80 elements. Creating vector isusTemp with 80 elements. Creating vector time with 80 elements. Creating vector isusQuality with 80 elements. Creating vector time with 80 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/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/2004/2004345/2004.345.06/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_2004.345.06.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2004.345.07 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.07/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.07/ 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/2004/2004345/2004.345.07/navigation.nc') Creating vector time with 790 elements. Creating vector mPos_x with 790 elements. Creating vector time with 790 elements. Creating vector mPos_y with 790 elements. Creating vector time with 790 elements. Creating vector mDepth with 790 elements. Creating vector time with 790 elements. Creating vector mGpsNorth with 790 elements. Creating vector time with 790 elements. Creating vector mGpsEast with 790 elements. Creating vector time with 790 elements. Creating vector mGpsValid with 790 elements. Creating vector time with 790 elements. Creating vector mPhi with 790 elements. Creating vector time with 790 elements. Creating vector mTheta with 790 elements. Creating vector time with 790 elements. Creating vector mPsi with 790 elements. Creating vector time with 790 elements. Creating vector mOmega_x with 790 elements. Creating vector time with 790 elements. Creating vector mOmega_y with 790 elements. Creating vector time with 790 elements. Creating vector mOmega_z with 790 elements. Creating vector time with 790 elements. Creating vector mPsaRange with 790 elements. Creating vector time with 790 elements. Creating vector mAltitude with 790 elements. Creating vector time with 790 elements. Creating vector mWaterSpeed with 790 elements. Creating vector time with 790 elements. Creating vector mDvlValid with 790 elements. Creating vector time with 790 elements. Creating vector mDvlNewData with 790 elements. Creating vector time with 790 elements. Creating vector mDeltaT with 790 elements. Creating vector time with 790 elements. Creating vector latitude with 790 elements. Creating vector time with 790 elements. Creating vector longitude with 790 elements. Creating vector time with 790 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.07/navigation.nc'); processNav(): median of positive valued depths = 3.1389 processNav(): Finding depths less than 21.9721 and times > 0 processNav(): length(Nav.depth) = 790 processNav(): length(gindx) = 790 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/2004/2004345/2004.345.07/gps.nc') Creating vector time with 120 elements. Creating vector hours with 120 elements. Creating vector time with 120 elements. Creating vector minutes with 120 elements. Creating vector time with 120 elements. Creating vector seconds with 120 elements. Creating vector time with 120 elements. Creating vector centiSeconds with 120 elements. Creating vector time with 120 elements. Creating vector latitude with 120 elements. Creating vector time with 120 elements. Creating vector longitude with 120 elements. Creating vector time with 120 elements. Creating vector quality with 120 elements. Creating vector time with 120 elements. Creating vector numberOfSatellites with 120 elements. Creating vector time with 120 elements. Creating vector hdop with 120 elements. Creating vector time with 120 elements. Creating vector antennaHeight with 120 elements. Creating vector time with 120 elements. Creating vector geoHeight with 120 elements. Creating vector time with 120 elements. Creating vector dgpsDataAge with 120 elements. Creating vector time with 120 elements. Creating vector dgpsRSID with 120 elements. Creating vector time with 120 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/parosci.nc') Creating vector time with 896 elements. Creating vector depth with 896 elements. Creating vector time with 896 elements. Creating vector temp with 896 elements. Creating vector time with 896 elements. Creating vector pressure with 896 elements. Creating vector time with 896 elements. Creating vector temp_period with 896 elements. Creating vector time with 896 elements. Creating vector pres_period with 896 elements. Creating vector time with 896 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.07/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.23066 max(Depth.data) = 7.5719 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.23066 max(Depth.data) = 7.5719 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/2004/2004345/2004.345.07/hydroscatlog.nc') Creating vector time with 703 elements. Creating vector Seconds with 703 elements. Creating vector time with 703 elements. Creating vector HundrethsOfSeconds with 703 elements. Creating vector time with 703 elements. Creating vector Snorm1 with 703 elements. Creating vector time with 703 elements. Creating vector Snorm2 with 703 elements. Creating vector time with 703 elements. Creating vector Snorm3 with 703 elements. Creating vector time with 703 elements. Creating vector Gain_Status_1 with 703 elements. Creating vector time with 703 elements. Creating vector Gain_Status_2 with 703 elements. Creating vector time with 703 elements. Creating vector Gain_Status_3 with 703 elements. Creating vector time with 703 elements. Creating vector RawDepthValue with 703 elements. Creating vector time with 703 elements. Creating vector RawTempValue with 703 elements. Creating vector time with 703 elements. Creating vector Temperature with 703 elements. Creating vector time with 703 elements. Creating vector ErrorValue with 703 elements. Creating vector time with 703 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/ctdDriver.nc') Creating vector time with 646 elements. Creating vector conductivity with 646 elements. Creating vector time with 646 elements. Creating vector temperature with 646 elements. Creating vector time with 646 elements. Creating vector cond_frequency with 646 elements. Creating vector time with 646 elements. Creating vector temp_frequency with 646 elements. Creating vector time with 646 elements. Creating vector spare with 646 elements. Creating vector time with 646 elements. Creating vector humidity with 646 elements. Creating vector time with 646 elements. Creating vector flow1 with 646 elements. Creating vector time with 646 elements. Creating vector OBS with 646 elements. Creating vector time with 646 elements. Creating vector dissolvedO2 with 646 elements. Creating vector time with 646 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.07/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/ctdDriver2.nc') Creating vector time with 671 elements. Creating vector conductivity with 671 elements. Creating vector time with 671 elements. Creating vector temperature with 671 elements. Creating vector time with 671 elements. Creating vector cond_frequency with 671 elements. Creating vector time with 671 elements. Creating vector temp_frequency with 671 elements. Creating vector time with 671 elements. Creating vector flow2 with 671 elements. Creating vector time with 671 elements. Creating vector spare with 671 elements. Creating vector time with 671 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.07/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/isuslog.nc') Creating vector time with 67 elements. Creating vector isusNitrate with 67 elements. Creating vector time with 67 elements. Creating vector isusTemp with 67 elements. Creating vector time with 67 elements. Creating vector isusQuality with 67 elements. Creating vector time with 67 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/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/2004/2004345/2004.345.07/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_2004.345.07.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Processing AUV mission: 2004.345.08 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.08/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.08/ 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/2004/2004345/2004.345.08/navigation.nc') Creating vector time with 815 elements. Creating vector mPos_x with 815 elements. Creating vector time with 815 elements. Creating vector mPos_y with 815 elements. Creating vector time with 815 elements. Creating vector mDepth with 815 elements. Creating vector time with 815 elements. Creating vector mGpsNorth with 815 elements. Creating vector time with 815 elements. Creating vector mGpsEast with 815 elements. Creating vector time with 815 elements. Creating vector mGpsValid with 815 elements. Creating vector time with 815 elements. Creating vector mPhi with 815 elements. Creating vector time with 815 elements. Creating vector mTheta with 815 elements. Creating vector time with 815 elements. Creating vector mPsi with 815 elements. Creating vector time with 815 elements. Creating vector mOmega_x with 815 elements. Creating vector time with 815 elements. Creating vector mOmega_y with 815 elements. Creating vector time with 815 elements. Creating vector mOmega_z with 815 elements. Creating vector time with 815 elements. Creating vector mPsaRange with 815 elements. Creating vector time with 815 elements. Creating vector mAltitude with 815 elements. Creating vector time with 815 elements. Creating vector mWaterSpeed with 815 elements. Creating vector time with 815 elements. Creating vector mDvlValid with 815 elements. Creating vector time with 815 elements. Creating vector mDvlNewData with 815 elements. Creating vector time with 815 elements. Creating vector mDeltaT with 815 elements. Creating vector time with 815 elements. Creating vector latitude with 815 elements. Creating vector time with 815 elements. Creating vector longitude with 815 elements. Creating vector time with 815 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.08/navigation.nc'); processNav(): median of positive valued depths = 3.0933 processNav(): Finding depths less than 21.6529 and times > 0 processNav(): length(Nav.depth) = 815 processNav(): length(gindx) = 815 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/2004/2004345/2004.345.08/gps.nc') Creating vector time with 111 elements. Creating vector hours with 111 elements. Creating vector time with 111 elements. Creating vector minutes with 111 elements. Creating vector time with 111 elements. Creating vector seconds with 111 elements. Creating vector time with 111 elements. Creating vector centiSeconds with 111 elements. Creating vector time with 111 elements. Creating vector latitude with 111 elements. Creating vector time with 111 elements. Creating vector longitude with 111 elements. Creating vector time with 111 elements. Creating vector quality with 111 elements. Creating vector time with 111 elements. Creating vector numberOfSatellites with 111 elements. Creating vector time with 111 elements. Creating vector hdop with 111 elements. Creating vector time with 111 elements. Creating vector antennaHeight with 111 elements. Creating vector time with 111 elements. Creating vector geoHeight with 111 elements. Creating vector time with 111 elements. Creating vector dgpsDataAge with 111 elements. Creating vector time with 111 elements. Creating vector dgpsRSID with 111 elements. Creating vector time with 111 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/parosci.nc') Creating vector time with 921 elements. Creating vector depth with 921 elements. Creating vector time with 921 elements. Creating vector temp with 921 elements. Creating vector time with 921 elements. Creating vector pressure with 921 elements. Creating vector time with 921 elements. Creating vector temp_period with 921 elements. Creating vector time with 921 elements. Creating vector pres_period with 921 elements. Creating vector time with 921 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.08/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.16106 max(Depth.data) = 8.3255 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.16106 max(Depth.data) = 8.3255 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/2004/2004345/2004.345.08/hydroscatlog.nc') Creating vector time with 722 elements. Creating vector Seconds with 722 elements. Creating vector time with 722 elements. Creating vector HundrethsOfSeconds with 722 elements. Creating vector time with 722 elements. Creating vector Snorm1 with 722 elements. Creating vector time with 722 elements. Creating vector Snorm2 with 722 elements. Creating vector time with 722 elements. Creating vector Snorm3 with 722 elements. Creating vector time with 722 elements. Creating vector Gain_Status_1 with 722 elements. Creating vector time with 722 elements. Creating vector Gain_Status_2 with 722 elements. Creating vector time with 722 elements. Creating vector Gain_Status_3 with 722 elements. Creating vector time with 722 elements. Creating vector RawDepthValue with 722 elements. Creating vector time with 722 elements. Creating vector RawTempValue with 722 elements. Creating vector time with 722 elements. Creating vector Temperature with 722 elements. Creating vector time with 722 elements. Creating vector ErrorValue with 722 elements. Creating vector time with 722 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/ctdDriver.nc') Creating vector time with 664 elements. Creating vector conductivity with 664 elements. Creating vector time with 664 elements. Creating vector temperature with 664 elements. Creating vector time with 664 elements. Creating vector cond_frequency with 664 elements. Creating vector time with 664 elements. Creating vector temp_frequency with 664 elements. Creating vector time with 664 elements. Creating vector spare with 664 elements. Creating vector time with 664 elements. Creating vector humidity with 664 elements. Creating vector time with 664 elements. Creating vector flow1 with 664 elements. Creating vector time with 664 elements. Creating vector OBS with 664 elements. Creating vector time with 664 elements. Creating vector dissolvedO2 with 664 elements. Creating vector time with 664 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.08/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/ctdDriver2.nc') Creating vector time with 691 elements. Creating vector conductivity with 691 elements. Creating vector time with 691 elements. Creating vector temperature with 691 elements. Creating vector time with 691 elements. Creating vector cond_frequency with 691 elements. Creating vector time with 691 elements. Creating vector temp_frequency with 691 elements. Creating vector time with 691 elements. Creating vector flow2 with 691 elements. Creating vector time with 691 elements. Creating vector spare with 691 elements. Creating vector time with 691 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.08/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/isuslog.nc') Creating vector time with 70 elements. Creating vector isusNitrate with 70 elements. Creating vector time with 70 elements. Creating vector isusTemp with 70 elements. Creating vector time with 70 elements. Creating vector isusQuality with 70 elements. Creating vector time with 70 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/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/2004/2004345/2004.345.08/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_2004.345.08.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_2004.345.01.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.02.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.03.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.04.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.05.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.06.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.07.mat Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.08.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 15 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_345_01_345_08_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_345_01_345_08.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_345_01_345_08.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 = 210 Gridding with nix = 630, 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 bbp676 fl676_uncorr N [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 304) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] 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 106761 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 106761 points from grid Monterey25.grd (2876 x 2447) Executing: /bin/rm -f ../results/2004345_GulperTimes.txt && touch ../results/2004345_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/2004/2004345/2004.345.01/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004345/2004.345.01/syslog -startEsecs 1102720157.0068 -surveyName Dorado389_2004_345_01_345_08 >> ../results/2004345_GulperTimes.txt Executing: removeGulpDups.py ../results/2004345_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/2004/2004345/2004.345.02/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004345/2004.345.02/syslog -startEsecs 1102720157.0068 -surveyName Dorado389_2004_345_01_345_08 >> ../results/2004345_GulperTimes.txt Executing: removeGulpDups.py ../results/2004345_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/2004/2004345/2004.345.03/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004345/2004.345.03/syslog -startEsecs 1102720157.0068 -surveyName Dorado389_2004_345_01_345_08 >> ../results/2004345_GulperTimes.txt Executing: removeGulpDups.py ../results/2004345_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/2004/2004345/2004.345.04/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004345/2004.345.04/syslog -startEsecs 1102720157.0068 -surveyName Dorado389_2004_345_01_345_08 >> ../results/2004345_GulperTimes.txt Executing: removeGulpDups.py ../results/2004345_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/2004/2004345/2004.345.05/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004345/2004.345.05/syslog -startEsecs 1102720157.0068 -surveyName Dorado389_2004_345_01_345_08 >> ../results/2004345_GulperTimes.txt Executing: removeGulpDups.py ../results/2004345_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/2004/2004345/2004.345.06/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004345/2004.345.06/syslog -startEsecs 1102720157.0068 -surveyName Dorado389_2004_345_01_345_08 >> ../results/2004345_GulperTimes.txt Executing: removeGulpDups.py ../results/2004345_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/2004/2004345/2004.345.07/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004345/2004.345.07/syslog -startEsecs 1102720157.0068 -surveyName Dorado389_2004_345_01_345_08 >> ../results/2004345_GulperTimes.txt Executing: removeGulpDups.py ../results/2004345_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/2004/2004345/2004.345.08/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2004/2004345/2004.345.08/syslog -startEsecs 1102720157.0068 -surveyName Dorado389_2004_345_01_345_08 >> ../results/2004345_GulperTimes.txt Executing: removeGulpDups.py ../results/2004345_GulperTimes.txt Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_345_01_345_08_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 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 gB470 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB676 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_2004_345_01_345_08_2column.png Elapsed time to save image: 8 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 gB470 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB676 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_2004_345_01_345_08_biolume.png Elapsed time to save image: 29 seconds 2Column contouring gridded variable gLOPCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCtransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCnonTransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCLCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gB470 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB676 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_2004_345_01_345_08_lopc.png Elapsed time to save image: 7 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_345_01_345_08_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_345_01_345_08_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_345_01_345_08_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_345_01_345_08_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_345_01_345_08_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_345_01_345_08_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_345_01_345_08_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_345_01_345_08_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_345_01_345_08_Temperature.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_345_01_345_08_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_345_01_345_08_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_345_01_345_08_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); 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 Nitrate 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_345_01_345_08_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_345_01_345_08_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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_345_01_345_08_Optical_Backscatter_470_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_345_01_345_08_Optical_Backscatter_470_nm.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 @676 nm', jetplus, varlimits(6,:), hs2.bbp676, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_345_01_345_08_Optical_Backscatter_676_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_345_01_345_08_Optical_Backscatter_676_nm.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, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl676_uncorr, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_345_01_345_08_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_345_01_345_08_Chlorophyll_Fluorescence.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, '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_345_01_345_08_Bioluminescence.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_345_01_345_08_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_345_01_345_08_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2004_345_01_345_08_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_345_01_345_08.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_345_01_345_08.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_345_01_345_08_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_345_01_345_08.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1173 NaNs found in bbpBlue. Interpolating anyway. 1533 NaNs found in bbpRed. Interpolating anyway. 1 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 404 NaN values in array of lon that is 14057 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 13653 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 13653 are not equal to number of Lat lon points = 14057 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_345_01_345_08.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_345_01_345_08.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_345_01_345_08_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_345_01_345_08_Gulper.txt’: No such file or directory ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1173 NaNs found in bbpBlue. Interpolating anyway. 1533 NaNs found in bbpRed. Interpolating anyway. 1 NaNs found in flRed_uncorr. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004_345_01_345_08_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_345_01_345_08.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_345_01_345_08_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_345_01_345_08.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_345_01_345_08 processed" mccann@mbari.org < mail_Dorado389_2004_345_01_345_08.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.01.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.02.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.03.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.04.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.05.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.06.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.07.mat /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2004.345.08.mat Processing time: 123 seconds