2014-06-08 12:48:36,689 DEBUG root about to write control file parameters to --yearbase 2014 --cruisename NH1410 --configtype python --sonar os75nb --dbname a_nh --datatype uhdas --cfgpath /home/data/NH1410/proc/os75nb/config --ens_len 300 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea --skip_avg ## see above --max_search_depth 1500 --proc_engine python --incremental --find_pflags --hidedisplay --top_plotbin 1 --auto 2014-06-08 12:48:36,690 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d os75nb 2014-06-08 12:48:36,690 DEBUG quick_adcp progdir = /home/currents/programs 2014-06-08 12:48:36,690 DEBUG quick_adcp binos = lnx64 2014-06-08 12:48:36,692 DEBUG quick_setup found cruise_info.hcorr (ashtech, adu, 0) 2014-06-08 12:48:36,692 INFO quick_adcp importing numpy 2014-06-08 12:48:36,708 INFO quick_adcp importing matplotlib 2014-06-08 12:48:36,853 DEBUG quick_mpl in Q_mpl 2014-06-08 12:48:36,853 DEBUG quick_adcp ------processor dictionary:------ __doc__ __init__ __module__ aflagit_setup as_cont as_nav as_vect asetup catnav check_beamangle check_dbinfo check_headcorr check_opts check_uhdascfg clearflags ddtime def_qlist del_overlapping fill_thisload_timerange get_asvars get_cmd_timerange get_nodb_times get_time_range getmat ldcodas listblocks llgrid loadping lst_btrk lst_conf lst_hdg lst_temp mpltest norotate opts plotbtcal_mpl plothcorr_mpl plotnav_mpl plotrefl_mpl plottemp_mpl plotwtcal_mpl putnav refabs refabsbt rotate rotated run_adcpsect run_applyedit run_autoedit_npy run_calc run_calib run_editsetup run_findpflags run_getheadcorr run_getnav run_guess_xducerxy run_guess_xducerxy_npy run_loaddb run_loadlta_npy run_loadping run_lstconfig run_lsthdg run_lsttemp run_matbincmd run_matfiles run_pingavg_npy run_plotter run_putnav run_py_codaseditsetup run_py_findpflags run_py_pingeditsetup run_pybincmd_lta run_pybincmd_uhdas run_pygbin_npy run_refabs run_refplots run_refsm run_refsm_npy run_rotate run_scanbin_npy run_scandata run_scanlta_npy run_scanping_npy run_setflags run_smoothr run_updategbin run_updatepygbin run_xducerxy run_xducerxy_npy scanping setflags smoothr timegrid timslip ubprint write_codas_editdefaults write_ping_editdefaults write_timerange_file zapsetup 2014-06-08 12:48:36,853 INFO quick_adcp cwd is /home/data/NH1410/proc/os75nb about to run these steps: - editsetup - scandata - avg_and_load - setflags - getnav - get_headcorr - rotate - adcpsect - refabs - smoothnav - putnav - refplots - find_pflags - apply_edit - navsteps - lst_temp - calib - matfiles - find_pflags 2014-06-08 12:48:36,853 INFO quick_adcp original fix file is a_nh.gps 2014-06-08 12:48:36,853 INFO quick_adcp smoothed nav file is a_nh_refsm.asc 2014-06-08 12:48:36,853 DEBUG quick_asect extracting matlab files for os75, nb pings 2014-06-08 12:48:36,872 DEBUG quick_setup data directory: /home/data/NH1410/raw/os75 2014-06-08 12:48:36,875 INFO quick_setup found 348 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/NH1410/raw/os75/*.raw" 2014-06-08 12:48:36,876 DEBUG quick_setup found 348 files from original filelist 2014-06-08 12:48:36,876 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/NH1410/raw/os75/nh2014_129_58290.raw ... 2014-06-08 12:48:36,878 DEBUG quick_adcp Sun Jun 8 12:48:36 2014 running quick_adcp.py as follows: --cntfile /home/data/NH1410/proc/os75nb/os75nb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_nh dbpath ../adcpdb deeper_boundaries [50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775] firstdepth 28 gridnum 80 increment 10 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2014 rl_endbin 20 rl_startbin 2 ss_string separate timegrid 60 vbasename vector ----- quick_adcp.py variables and current values ------ adjust_time 1 auto True badbeam None beamangle 30 best_loggerdday_name unix_dday best_utcdday_name dday bindir /home/currents/programs/codas3/bin/lnx64 binos lnx64 btrk_step 1 cfgpath /home/data/NH1410/proc/os75nb/config cntfile /home/data/NH1410/proc/os75nb/os75nb_qpy.cnt commands None configtype python cruisename NH1410 data_def vmadcp.def datadir /home/data/NH1410/raw/os75 datafile_glob *.raw datatype uhdas dbname a_nh dday_bailout None debug False diarystr %% no diary written %% displaystr set(0,'defaultfigureposition',[0 0 300 400]) set(0,'defaultfiguremenubar','none') set(0,'defaultfiguretoolbar','none') ducer_depth None editcfg_file override_editcfg enddday_file None ens_halign None ens_len 300 ensgyrorbin False expert None filelist ['/home/data/NH1410/raw/os75/nh2014_129_58290.raw', '/home/data/NH1410/raw/os75/nh2014_129_64800.raw', '/home/data/NH1410/raw/os75/nh2014_129_72000.raw', '/home/data/NH1410/raw/os75/nh2014_129_79200.raw', '/home/data/NH1410/raw/os75/nh2014_130_00000.raw', 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'/home/data/NH1410/raw/os75/nh2014_158_43200.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 28 fixfile a_nh.gps frequency 75 gbin_style python gbindirbase /home/data/NH1410/gbin hcorr_inst ashtech help False hidedisplay True incremental True instname os75 jitter 15 max_BLKprofiles 300 max_search_depth 1500 maxrunsecs None min_filter_fraction 0.5 model os nosave_editcfg 0 num_persistence 24 numbins 128 overview False pgmin 50 ping_headcorr False pingtype nb post_headcorr None printformats png proc_engine python proc_yearbase 2014 progdir /home/currents/programs py_gbindirbase /home/data/NH1410/gbin rawstd_cutoff None rl_endbin 20 rl_startbin 2 rotate_amplitude 1 rotate_angle 0 rotate_file None save_editcfg 1 save_lastens 0 setup_info False skip_avg True smfile a_nh_refsm.asc sonar os75nb steps2rerun timeout_secs 86400 tips False tktail False top_plotbin 1 ub_type 1920 update_gbin False use_refsm True use_smoothr False vardoc False varvals False wtrk_step 7 xducer_dx None xducer_dy None yearbase 2014 configured to run the following steps: editsetup scandata avg_and_load setflags getnav get_headcorr rotate adcpsect refabs smoothnav putnav refplots find_pflags apply_edit navsteps lst_temp calib matfiles find_pflags 2014-06-08 12:48:36,878 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:36,878 INFO quick_adcp step 1: set up editing files 2014-06-08 12:48:36,878 DEBUG quick_run executing commands from /home/data/NH1410/proc/os75nb/edit 2014-06-08 12:48:36,878 DEBUG quick_run setup.m exists. not replacing 2014-06-08 12:48:36,878 DEBUG quick_run asetup.m exists. not replacing 2014-06-08 12:48:36,878 DEBUG quick_run aflagit_setup.m exists. not replacing 2014-06-08 12:48:36,878 DEBUG quick_subs dbname: ../adcpdb/a_nh pg_min: 50 clear_range /* reset range */ clear_all_bits /* clear flags except pg_min*/ clear_bad_profile /* reset access vars lgb */ time_ranges: all 2014-06-08 12:48:36,878 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:36,879 INFO quick_adcp step 2: scan files for time range 2014-06-08 12:48:36,879 INFO quick_adcp about to run numpy scan, requiring python gbins 2014-06-08 12:48:36,879 DEBUG quick_npy Starting: scanping 2014-06-08 12:48:37,259 DEBUG quick_npy Ending: scanping 2014-06-08 12:48:37,260 DEBUG quick_subs start_end_time 2014/05/10 16:12:07 to 2014/05/10 16:37:20 2014-06-08 12:48:37,260 DEBUG quick_subs dd0: 129.675081 dd1: 129.692593 2014-06-08 12:48:37,260 INFO quick_adcp in quick_adcp.py: after scan; look for database times in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:37,260 INFO quick_adcp looking for database with adcpdb/a_nh*.blk 2014-06-08 12:48:37,261 INFO quick_adcp database found: listing blocks 2014-06-08 12:48:37,261 DEBUG quick_subs removing a_nhdir.blk 2014-06-08 12:48:37,261 DEBUG quick_subs about to run mkblkdir 2014-06-08 12:48:37,261 DEBUG quick_subs database still exists; rerunning mkdirblk 2014-06-08 12:48:37,261 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2014-06-08 12:48:37,273 DEBUG quick_subs database passes. 2014-06-08 12:48:37,274 DEBUG quick_subs start_end_time 2014/05/10 16:17:06 to 2014/06/08 12:17:38 2014-06-08 12:48:37,274 DEBUG quick_subs dd0: 129.678542 dd1: 158.512245 2014-06-08 12:48:37,274 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2014-06-08 12:48:37,274 DEBUG quick_adcp origdb_time_range is 2014/05/10 16:17:06 to 2014/06/08 12:17:38 2014-06-08 12:48:37,274 DEBUG quick_adcp (129.678542 to 158.512245) 2014-06-08 12:48:37,274 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:37,274 INFO quick_adcp step 3: generate averaged data... 2014-06-08 12:48:37,275 DEBUG quick_run file load/ping_editparams.txt exists. not replacing 2014-06-08 12:48:37,275 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:37,275 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/load 2014-06-08 12:48:37,275 DEBUG quick_setup running python command "run_pingavg_npy" 2014-06-08 12:48:37,275 DEBUG quick_npy Starting: pingavg 2014-06-08 12:48:37,276 DEBUG quick_npy singleping editing parameters: 2014-06-08 12:48:37,277 DEBUG quick_npy bigtarget_mab_window : 11 2014-06-08 12:48:37,277 DEBUG quick_npy rl_endbin : 20 2014-06-08 12:48:37,277 DEBUG quick_npy max_search_depth : 1500 2014-06-08 12:48:37,277 DEBUG quick_npy cor_cutoff : 120 2014-06-08 12:48:37,277 DEBUG quick_npy ampfilt : 40 2014-06-08 12:48:37,277 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2014-06-08 12:48:37,277 DEBUG quick_npy rl_startbin : 2 2014-06-08 12:48:37,277 DEBUG quick_npy ecutoff : 1 2014-06-08 12:48:37,277 DEBUG quick_npy refavg_valcutoff : 1 2014-06-08 12:48:37,277 DEBUG quick_npy weakprof_percent : 30 2014-06-08 12:48:37,277 DEBUG quick_npy bigtarget_ampthresh : 55 2014-06-08 12:48:37,283 INFO pingavg Pingavg.run for time range 158.501105 to 158.533224 2014-06-08 12:48:37,308 DEBUG pingavg Chunk 1 of 1, 158.501105 to 158.533224 2014-06-08 12:48:37,308 DEBUG pingavg Nothing written 2014-06-08 12:48:37,308 DEBUG quick_npy wrote 0 averages 2014-06-08 12:48:37,309 DEBUG quick_npy Ending: pingavg 2014-06-08 12:48:37,309 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:37,309 INFO quick_adcp step 4: load averaged data (to database) 2014-06-08 12:48:37,310 DEBUG quick_subs in del_overlapping 2014-06-08 12:48:37,310 DEBUG quick_subs lastblock: 2014-06-08 12:48:37,310 DEBUG quick_subs 29 2014-06-08 12:48:37,310 DEBUG quick_subs lastcmd: 2014-06-08 12:48:37,310 DEBUG quick_subs 29 2014-06-08 12:48:37,310 DEBUG quick_subs delblks: 2014-06-08 12:48:37,310 DEBUG quick_subs [29] 2014-06-08 12:48:37,310 DEBUG quick_subs loadblks: 2014-06-08 12:48:37,310 DEBUG quick_subs [29] 2014-06-08 12:48:37,311 DEBUG quick_subs about to run mkblkdir 2014-06-08 12:48:37,311 DEBUG quick_subs database still exists; rerunning mkdirblk 2014-06-08 12:48:37,311 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2014-06-08 12:48:37,323 DEBUG quick_subs database passes. 2014-06-08 12:48:37,324 DEBUG quick_subs start_end_time 2014/05/10 16:17:06 to 2014/06/07 19:47:39 2014-06-08 12:48:37,324 DEBUG quick_subs dd0: 129.678542 dd1: 157.824757 2014-06-08 12:48:37,324 DEBUG quick_run [29] 2014-06-08 12:48:37,324 DEBUG quick_run cmdlist 2014-06-08 12:48:37,324 DEBUG quick_run ['./ens_blk029.cmd'] 2014-06-08 12:48:37,326 INFO quick_run Warning: 1 files will be loaded; 29 already exist 2014-06-08 12:48:37,326 INFO quick_run Sun Jun 8 12:48:37 2014 2014-06-08 12:48:37,326 INFO quick_run about to load uhdas files 2014-06-08 12:48:37,326 INFO quick_run /home/data/NH1410/raw/os75/nh2014_129_58290.raw /home/data/NH1410/raw/os75/nh2014_129_64800.raw /home/data/NH1410/raw/os75/nh2014_129_72000.raw /home/data/NH1410/raw/os75/nh2014_129_79200.raw /home/data/NH1410/raw/os75/nh2014_130_00000.raw ... 2014-06-08 12:48:37,326 DEBUG quick_setup load/ldcodas.tmp exists 2014-06-08 12:48:37,326 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:37,327 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/load 2014-06-08 12:48:37,327 DEBUG quick_setup running python command "ldcodas" 2014-06-08 12:48:37,327 DEBUG quick_subs filling "thisload" timerange 2014-06-08 12:48:37,328 DEBUG quick_subs in ldcodas 2014-06-08 12:48:37,328 DEBUG quick_subs cmdlist: 2014-06-08 12:48:37,328 DEBUG quick_subs ['./ens_blk029.cmd'] 2014-06-08 12:48:37,328 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_nh DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2014 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk029.cmd 2014-06-08 12:48:37,328 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/ldcodas ldcodas.tmp 2014-06-08 12:48:37,357 DEBUG quick_subs removing a_nhdir.blk 2014-06-08 12:48:37,357 DEBUG quick_subs about to run mkblkdir 2014-06-08 12:48:37,357 DEBUG quick_subs database still exists; rerunning mkdirblk 2014-06-08 12:48:37,358 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2014-06-08 12:48:37,369 DEBUG quick_subs database passes. 2014-06-08 12:48:37,370 DEBUG quick_subs start_end_time 2014/05/10 16:17:06 to 2014/06/08 12:47:38 2014-06-08 12:48:37,370 DEBUG quick_subs dd0: 129.678542 dd1: 158.533079 2014-06-08 12:48:37,370 INFO quick_adcp loaded_time_range is 2014/05/10 16:17:06 to 2014/06/08 12:47:38 2014-06-08 12:48:37,370 INFO quick_adcp (129.678542 to 158.533079) 2014-06-08 12:48:37,370 INFO quick_adcp origdb_time_range is 2014/05/10 16:17:06 to 2014/06/08 12:17:38 2014-06-08 12:48:37,370 INFO quick_adcp (129.678542 to 158.512245) 2014-06-08 12:48:37,371 INFO quick_adcp thisload_time_range is 2014/06/07 19:52:39 to 2014/06/08 12:47:38 2014-06-08 12:48:37,371 INFO quick_adcp (157.828229 to 157.828229) 2014-06-08 12:48:37,371 INFO quick_adcp --------------------- 2014-06-08 12:48:37,371 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:37,371 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/adcpdb 2014-06-08 12:48:37,371 DEBUG quick_setup running python command "lst_conf" 2014-06-08 12:48:37,371 DEBUG quick_subs dbname: a_nh output: a_nh.cnh time_ranges: all 2014-06-08 12:48:37,371 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_conf lst_conf.tmp 2014-06-08 12:48:38,254 DEBUG quick_setup found (in edit/asetup.m): 2014-06-08 12:48:38,254 DEBUG quick_setup config.beamangle is 30 2014-06-08 12:48:38,254 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:38,254 INFO quick_adcp step 5: set up files for gautoedit.py 2014-06-08 12:48:38,254 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2014-06-08 12:48:38,254 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:38,255 INFO quick_adcp step 6: set up files for gautoedit.py 2014-06-08 12:48:38,255 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:38,255 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/edit 2014-06-08 12:48:38,255 DEBUG quick_setup running python command "setflags" 2014-06-08 12:48:38,255 DEBUG quick_subs dbname: ../adcpdb/a_nh pg_min: 50 set_range_bit time_ranges: all 2014-06-08 12:48:38,255 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2014-06-08 12:48:38,318 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:38,319 INFO quick_adcp step 7: get navigation 2014-06-08 12:48:38,319 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:38,319 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/nav 2014-06-08 12:48:38,319 DEBUG quick_setup running python command "catnav" 2014-06-08 12:48:38,322 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2014-06-08 12:48:38,323 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:38,323 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/cal/rotate 2014-06-08 12:48:38,323 DEBUG quick_setup running python command "lst_hdg" 2014-06-08 12:48:38,323 DEBUG quick_subs dbname: ../../adcpdb/a_nh output: scn.hdg step_size= 1 year_base= 2014 time_ranges: all 2014-06-08 12:48:38,323 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_hdg lst_hdg.tmp 2014-06-08 12:48:38,367 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:38,367 INFO quick_adcp step 8: get heading correction 2014-06-08 12:48:38,367 DEBUG quick_run hcorr_inst is ashtech 2014-06-08 12:48:38,367 DEBUG quick_mpl Starting plot: hcorr 2014-06-08 12:48:38,448 DEBUG quick_mplplots found 28.854538 days of data 2014-06-08 12:48:38,449 DEBUG quick_mplplots figures with 4 panels per page, 1.000000 days per panel 2014-06-08 12:48:38,449 DEBUG quick_mplplots printing 8 pages 2014-06-08 12:48:39,014 DEBUG quick_mpl Ending plot: hcorr 2014-06-08 12:48:39,014 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:39,014 INFO quick_adcp step 9: rotate velocities 2014-06-08 12:48:39,014 DEBUG quick_setup cal/rotate/norotate.tmp exists 2014-06-08 12:48:39,014 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:39,014 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/cal/rotate 2014-06-08 12:48:39,014 DEBUG quick_setup running python command "norotate" 2014-06-08 12:48:39,014 DEBUG quick_subs /* No rotation was done using the "rotate" command, but */ /* it is useful have the skeleton of a rotate.tmp file */ /* to edit, should the need arise. That is the purpose */ /* of this file. */ DB_NAME: ../../adcpdb/a_nh LOG_FILE: rotate.log TIME_RANGE: 2014/05/10 16:17:06 to 2014/06/08 12:47:38 OPTION_LIST: water_and_bottom_track: year_base= 2014 /* time_angle_file: time_angle.ang */ amplitude= 1.0 angle_0= 0.0 end end 2014-06-08 12:48:39,015 DEBUG quick_setup about to run echo "writing dummy rotate file" 2014-06-08 12:48:39,020 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:39,020 INFO quick_adcp step 10: nav steps: run adcpsect 2014-06-08 12:48:39,020 DEBUG quick_setup nav/as_nav.tmp exists 2014-06-08 12:48:39,020 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:39,021 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/nav 2014-06-08 12:48:39,021 DEBUG quick_setup running python command "as_nav" 2014-06-08 12:48:39,021 DEBUG quick_subs dbname: ../adcpdb/a_nh output: a_nh step_size: 1 ndepth: 20 time_ranges: separate year_base= 2014 option_list: pg_min= 50 navigation: reference_bins 2 to 20 end statistics: mean units= 0.01 /* cm/s instead of default m/s */ end flag_mask: ALL_BITS end end 2014/05/10 16:17:06 to 2014/06/08 12:47:38 /* the whole time range */ 2014-06-08 12:48:39,021 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2014-06-08 12:48:39,101 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:39,102 INFO quick_adcp step 11: nav steps: run refabs 2014-06-08 12:48:39,102 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:39,102 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/nav 2014-06-08 12:48:39,102 DEBUG quick_setup running python command "refabs" 2014-06-08 12:48:39,102 DEBUG quick_subs fix_file_type: simple reference_file: a_nh.nav fix_file: a_nh.gps output: a_nh.ref year_base= 2014 ensemble_length= 300 gap_tolerance= 10 2014-06-08 12:48:39,102 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2014-06-08 12:48:39,159 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:39,159 INFO quick_adcp step 12: nav steps: run smoothr for plots 2014-06-08 12:48:39,159 DEBUG quick_setup nav/smoothr.tmp exists 2014-06-08 12:48:39,160 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:39,160 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/nav 2014-06-08 12:48:39,160 DEBUG quick_setup running python command "smoothr" 2014-06-08 12:48:39,160 DEBUG quick_subs reference_file: a_nh.nav refabs_output: a_nh.ref output: a_nh.sm filter_hwidth= 0.0208 min_filter_fraction= 0.5 max_gap_ratio= 0.05 max_gap_distance= 50 max_gap_time= 30 /* 0.5 minutes */ ensemble_time= 300 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2014-06-08 12:48:39,160 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2014-06-08 12:48:39,465 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:39,465 INFO quick_adcp step 13: nav steps: smooth navigation 2014-06-08 12:48:39,465 INFO quick_adcp about to run numpy refsm 2014-06-08 12:48:39,465 DEBUG quick_npy Starting: refsm 2014-06-08 12:48:39,676 DEBUG nav dtmin = -0.50 dtmax = 4.05 2014-06-08 12:48:39,928 DEBUG quick_npy Ending: refsm 2014-06-08 12:48:39,928 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:39,928 INFO quick_adcp step 14: nav steps: put smoothed nav into codasdb 2014-06-08 12:48:39,928 DEBUG quick_setup nav/putnav.tmp exists 2014-06-08 12:48:39,929 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:39,929 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/nav 2014-06-08 12:48:39,929 DEBUG quick_setup running python command "putnav" 2014-06-08 12:48:39,929 DEBUG quick_subs dbname: ../adcpdb/a_nh position_file: a_nh_refsm.asc year_base= 2014 tolerance= 5 navigation_sources: gps end 2014-06-08 12:48:39,929 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2014-06-08 12:48:40,028 INFO quick_adcp plotting navigation 2014-06-08 12:48:40,028 DEBUG quick_mpl Starting plot: nav 2014-06-08 12:48:40,359 DEBUG quick_mpl Ending plot: nav 2014-06-08 12:48:40,360 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:40,360 INFO quick_adcp step 15: nav steps: make reflayer plots 2014-06-08 12:48:40,360 DEBUG quick_mpl Starting plot: refl 2014-06-08 12:48:40,540 DEBUG quick_mplplots found 28.847610 days of data 2014-06-08 12:48:40,540 DEBUG quick_mplplots start day is 129.000000 2014-06-08 12:48:40,540 DEBUG quick_mplplots figures with 2.000000 days per page 2014-06-08 12:48:40,541 DEBUG quick_mplplots printing 15 pages 2014-06-08 12:48:40,541 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2014-06-08 12:48:41,083 DEBUG quick_mpl Ending plot: refl 2014-06-08 12:48:41,084 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:41,086 INFO quick_adcp step 16: find profile flags 2014-06-08 12:48:41,087 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:41,087 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/edit 2014-06-08 12:48:41,087 DEBUG quick_setup running python command "run_autoedit_npy" 2014-06-08 12:48:41,087 DEBUG quick_npy Starting: autoedit 2014-06-08 12:48:41,321 DEBUG pingedit wrote 1 bad bins to abadbin_tmp.asc 2014-06-08 12:48:41,339 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2014-06-08 12:48:41,339 DEBUG quick_npy Ending: autoedit 2014-06-08 12:48:41,339 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:41,339 INFO quick_adcp step 17: apply editing 2014-06-08 12:48:41,339 DEBUG quick_run starting in: /home/data/NH1410/proc/os75nb 2014-06-08 12:48:41,339 DEBUG quick_run executing commands from: edit 2014-06-08 12:48:41,340 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/dbupdate ../adcpdb/a_nh abadprf_tmp.asc 2014-06-08 12:48:41,346 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/badbin ../adcpdb/a_nh abadbin_tmp.asc 2014-06-08 12:48:41,354 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/set_lgb ../adcpdb/a_nh 30 2014-06-08 12:48:41,360 DEBUG quick_subs dbname: ../adcpdb/a_nh pg_min: 50 set_range_bit time_ranges: all 2014-06-08 12:48:41,361 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2014-06-08 12:48:41,418 DEBUG quick_run changing directories back to /home/data/NH1410/proc/os75nb 2014-06-08 12:48:41,418 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:41,418 INFO quick_adcp step 18: run nav steps 2014-06-08 12:48:41,418 DEBUG quick_setup nav/as_nav.tmp exists 2014-06-08 12:48:41,418 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:41,419 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/nav 2014-06-08 12:48:41,419 DEBUG quick_setup running python command "as_nav" 2014-06-08 12:48:41,419 DEBUG quick_subs dbname: ../adcpdb/a_nh output: a_nh step_size: 1 ndepth: 20 time_ranges: separate year_base= 2014 option_list: pg_min= 50 navigation: reference_bins 2 to 20 end statistics: mean units= 0.01 /* cm/s instead of default m/s */ end flag_mask: ALL_BITS end end 2014/05/10 16:17:06 to 2014/06/08 12:47:38 /* the whole time range */ 2014-06-08 12:48:41,419 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2014-06-08 12:48:41,498 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:41,498 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/nav 2014-06-08 12:48:41,499 DEBUG quick_setup running python command "refabs" 2014-06-08 12:48:41,499 DEBUG quick_subs fix_file_type: simple reference_file: a_nh.nav fix_file: a_nh.gps output: a_nh.ref year_base= 2014 ensemble_length= 300 gap_tolerance= 10 2014-06-08 12:48:41,499 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2014-06-08 12:48:41,556 DEBUG quick_setup nav/smoothr.tmp exists 2014-06-08 12:48:41,556 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:41,557 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/nav 2014-06-08 12:48:41,557 DEBUG quick_setup running python command "smoothr" 2014-06-08 12:48:41,557 DEBUG quick_subs reference_file: a_nh.nav refabs_output: a_nh.ref output: a_nh.sm filter_hwidth= 0.0208 min_filter_fraction= 0.5 max_gap_ratio= 0.05 max_gap_distance= 50 max_gap_time= 30 /* 0.5 minutes */ ensemble_time= 300 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2014-06-08 12:48:41,557 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2014-06-08 12:48:41,860 DEBUG quick_npy Starting: refsm 2014-06-08 12:48:42,062 DEBUG nav dtmin = -0.50 dtmax = 4.05 2014-06-08 12:48:42,308 DEBUG quick_npy Ending: refsm 2014-06-08 12:48:42,309 DEBUG quick_setup nav/putnav.tmp exists 2014-06-08 12:48:42,309 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:42,309 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/nav 2014-06-08 12:48:42,309 DEBUG quick_setup running python command "putnav" 2014-06-08 12:48:42,309 DEBUG quick_subs dbname: ../adcpdb/a_nh position_file: a_nh_refsm.asc year_base= 2014 tolerance= 5 navigation_sources: gps end 2014-06-08 12:48:42,309 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2014-06-08 12:48:42,406 DEBUG quick_mpl Starting plot: nav 2014-06-08 12:48:42,741 DEBUG quick_mpl Ending plot: nav 2014-06-08 12:48:42,741 DEBUG quick_mpl Starting plot: refl 2014-06-08 12:48:42,923 DEBUG quick_mplplots found 28.847610 days of data 2014-06-08 12:48:42,923 DEBUG quick_mplplots start day is 129.000000 2014-06-08 12:48:42,923 DEBUG quick_mplplots figures with 2.000000 days per page 2014-06-08 12:48:42,924 DEBUG quick_mplplots printing 15 pages 2014-06-08 12:48:42,924 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2014-06-08 12:48:43,474 DEBUG quick_mpl Ending plot: refl 2014-06-08 12:48:43,475 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:43,475 INFO quick_adcp step 19: plot temperature 2014-06-08 12:48:43,475 DEBUG quick_setup edit/lst_temp.tmp exists 2014-06-08 12:48:43,475 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:43,475 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/edit 2014-06-08 12:48:43,475 DEBUG quick_setup running python command "lst_temp" 2014-06-08 12:48:43,475 DEBUG quick_subs dbname: ../adcpdb/a_nh output: a_nh.tem step_size= 1 year_base= 2014 time_ranges: all 2014-06-08 12:48:43,476 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_temp lst_temp.tmp 2014-06-08 12:48:43,523 DEBUG quick_mpl Starting plot: temp 2014-06-08 12:48:43,586 DEBUG quick_mplplots plotting 8308 points 2014-06-08 12:48:43,806 DEBUG quick_mpl Ending plot: temp 2014-06-08 12:48:43,806 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:43,806 INFO quick_adcp step 20: run calibration steps 2014-06-08 12:48:43,806 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2014-06-08 12:48:43,806 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:43,806 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/cal/botmtrk 2014-06-08 12:48:43,806 DEBUG quick_setup running python command "lst_btrk" 2014-06-08 12:48:43,807 DEBUG quick_subs dbname: ../../adcpdb/a_nh output: a_nh.btm step_size= 1 year_base= 2014 time_ranges: 2014/05/10 16:17:06 to 2014/06/08 12:47:38 /* whole time range */ 2014-06-08 12:48:43,807 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_btrk lst_btrk.tmp 2014-06-08 12:48:43,826 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2014-06-08 12:48:43,827 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:43,827 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/cal/botmtrk 2014-06-08 12:48:43,827 DEBUG quick_setup running python command "refabsbt" 2014-06-08 12:48:43,827 DEBUG quick_subs fix_file_type: simple reference_file: a_nh.btm fix_file: ../../nav/a_nh.gps output: a_nh.ref year_base= 2014 ensemble_length= 300 gap_tolerance= 60 2014-06-08 12:48:43,827 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabsbt refabsbt.tmp 2014-06-08 12:48:43,833 DEBUG quick_mpl Starting plot: btcal 2014-06-08 12:48:43,834 DEBUG quick_mplplots No data in a_nh.btm 2014-06-08 12:48:43,834 DEBUG quick_mplplots Returning from Btplot with no output 2014-06-08 12:48:43,834 DEBUG quick_mpl Ending plot: btcal 2014-06-08 12:48:43,834 DEBUG quick_setup nav/as_nav.tmp exists 2014-06-08 12:48:43,834 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:43,834 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/nav 2014-06-08 12:48:43,834 DEBUG quick_setup running python command "as_nav" 2014-06-08 12:48:43,834 DEBUG quick_subs dbname: ../adcpdb/a_nh output: a_nh step_size: 1 ndepth: 20 time_ranges: separate year_base= 2014 option_list: pg_min= 50 navigation: reference_bins 2 to 20 end statistics: mean units= 0.01 /* cm/s instead of default m/s */ end flag_mask: ALL_BITS end end 2014/05/10 16:17:06 to 2014/06/08 12:47:38 /* the whole time range */ 2014-06-08 12:48:43,835 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2014-06-08 12:48:43,916 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2014-06-08 12:48:43,916 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:43,916 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/cal/watertrk 2014-06-08 12:48:43,916 DEBUG quick_setup running python command "timslip" 2014-06-08 12:48:43,916 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_nh.gps reference_file: ../../nav/a_nh.nav output_file: a_nh_7.cal year_base= 2014 min_n_fixes= 7 /* 5 7 9 */ n_refs= 7 /* 5 7 9 */ i_ref_l0= 1 i_ref_l1= 2 /* 1 2 3 */ i_ref_r0= 5 /* 4 5 6 */ i_ref_r1= 6 /* 4 6 8 */ up_thresh= 3.0 /* m/s */ down_thresh= 3.0 /* m/s */ turn_speed= 2.0 /* m/s */ turn_thresh= 60 /* degrees */ dtmax= 360 /* seconds, for 300-second ensembles */ tolerance= 5.e-5 /* days, about 5 seconds */ grid: ensemble use_shifted_times? no 2014-06-08 12:48:43,916 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timslip timslip.tmp 2014-06-08 12:48:43,942 DEBUG quick_mpl Starting plot: wtcal 2014-06-08 12:48:43,944 DEBUG quick_mplplots Found 86 calibration points 2014-06-08 12:48:44,576 DEBUG quick_mpl Ending plot: wtcal 2014-06-08 12:48:44,576 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:44,576 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/cal/watertrk 2014-06-08 12:48:44,576 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2014-06-08 12:48:44,576 DEBUG quick_npy Starting: guess_xducerxy 2014-06-08 12:48:44,800 DEBUG quick_npy Ending: guess_xducerxy 2014-06-08 12:48:44,800 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:44,800 INFO quick_adcp step 21: extract matlab "allbins" 2014-06-08 12:48:44,800 DEBUG quick_asect ------------ step 18: make matlab files for plotting ------------- 2014-06-08 12:48:44,800 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:44,801 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/vector 2014-06-08 12:48:44,801 DEBUG quick_setup running python command "timegrid" 2014-06-08 12:48:44,801 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_nh.tmp 2014-06-08 12:48:44,811 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:44,811 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/vector 2014-06-08 12:48:44,811 DEBUG quick_setup running python command "as_vect" 2014-06-08 12:48:44,811 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_vect.tmp 2014-06-08 12:48:44,936 DEBUG quick_asect done making vector matfiles 2014-06-08 12:48:44,936 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:44,936 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/contour 2014-06-08 12:48:44,936 DEBUG quick_setup running python command "timegrid" 2014-06-08 12:48:44,937 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_nh.tmp 2014-06-08 12:48:44,952 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:44,953 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/contour 2014-06-08 12:48:44,953 DEBUG quick_setup running python command "as_cont" 2014-06-08 12:48:44,953 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_cont.tmp 2014-06-08 12:48:45,144 DEBUG quick_setup starting in /home/data/NH1410/proc/os75nb 2014-06-08 12:48:45,144 DEBUG quick_setup executing commands from /home/data/NH1410/proc/os75nb/contour 2014-06-08 12:48:45,145 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_nh 2014-06-08 12:48:45,636 DEBUG quick_asect done running getmat with "allbins" 2014-06-08 12:48:45,636 INFO quick_adcp --------------------------------------------- 2014-06-08 12:48:45,636 INFO quick_adcp step 22: write "cruise_info.txt" 2014-06-08 12:48:45,653 INFO root copying NOFIG to /home/adcp/www/figures/os75nb_hcorr_plot.png 2014-06-08 12:48:45,653 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os75nb_hcorr_plot_thumb.png 2014-06-08 12:48:45,653 DEBUG root matfile is contour/contour_uv.mat 2014-06-08 12:48:45,664 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os75nb_cont_uv.mat 2014-06-08 12:48:45,664 DEBUG root matfile is vector/vector_uv.mat 2014-06-08 12:48:45,665 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os75nb_vect_uv.mat 2014-06-08 12:48:45,665 DEBUG root matfile is contour/contour_xy.mat 2014-06-08 12:48:45,665 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os75nb_cont_xy.mat 2014-06-08 12:48:45,666 DEBUG root matfile is vector/vector_xy.mat 2014-06-08 12:48:45,666 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os75nb_vect_xy.mat 2014-06-08 12:48:45,666 DEBUG root about to copy file edit/a_nh.tem to /home/adcp/www/data/os75nb_temp.asc 2014-06-08 12:48:45,667 INFO root copying edit/a_nh.tem to /home/adcp/www/data/os75nb_temp.asc 2014-06-08 12:48:47,878 DEBUG root about to copy netcdf file /home/data/NH1410/proc/os75nb/contour/os75nb.nc to /home/adcp/www/data/os75nb.nc 2014-06-08 12:48:47,902 INFO root copying edit/a_nh.tem to /home/adcp/www/data/os75nb.nc 2014-06-08 12:48:47,941 INFO root generating pingstats for os75nb 2014-06-08 12:48:47,941 INFO root Ending quick_adcp.py