2013-11-24 05:51:08,524 DEBUG root about to write control file parameters to --yearbase 2013 --cruisename SP1314 --configtype python --sonar nb300 --dbname a_sp --datatype uhdas --cfgpath /home/data/SP1314/proc/nb300/config --ens_len 120 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea --skip_avg ## see above --max_search_depth 300 --proc_engine python --incremental --find_pflags --hidedisplay --top_plotbin 1 --auto 2013-11-24 05:51:08,524 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d nb300 2013-11-24 05:51:08,525 DEBUG quick_adcp progdir = /home/currents/programs 2013-11-24 05:51:08,525 DEBUG quick_adcp binos = lnx64 2013-11-24 05:51:08,527 DEBUG quick_setup found cruise_info.hcorr (ashtech, adu, 0) 2013-11-24 05:51:08,528 INFO quick_adcp importing numpy 2013-11-24 05:51:08,542 INFO quick_adcp importing matplotlib 2013-11-24 05:51:08,684 DEBUG quick_mpl in Q_mpl 2013-11-24 05:51:08,684 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 2013-11-24 05:51:08,685 INFO quick_adcp cwd is /home/data/SP1314/proc/nb300 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 2013-11-24 05:51:08,685 INFO quick_adcp original fix file is a_sp.gps 2013-11-24 05:51:08,685 INFO quick_adcp smoothed nav file is a_sp_refsm.asc 2013-11-24 05:51:08,685 DEBUG quick_asect extracting matlab files for nb300, nb pings 2013-11-24 05:51:08,687 DEBUG quick_setup data directory: /home/data/SP1314/raw/nb300 2013-11-24 05:51:08,687 INFO quick_setup found 8 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/SP1314/raw/nb300/*.raw" 2013-11-24 05:51:08,687 DEBUG quick_setup found 8 files from original filelist 2013-11-24 05:51:08,688 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/SP1314/raw/nb300/sp2013_326_55267.raw ... 2013-11-24 05:51:08,688 DEBUG quick_adcp Sun Nov 24 05:51:08 2013 running quick_adcp.py as follows: --cntfile /home/data/SP1314/proc/nb300/nb300_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_sp dbpath ../adcpdb deeper_boundaries [40, 60, 80, 100, 120] firstdepth 11 gridnum 80 increment 2 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2013 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/SP1314/proc/nb300/config cntfile /home/data/SP1314/proc/nb300/nb300_qpy.cnt commands None configtype python cruisename SP1314 data_def vmadcp.def datadir /home/data/SP1314/raw/nb300 datafile_glob *.raw datatype uhdas dbname a_sp 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/SP1314/raw/nb300/sp2013_326_55267.raw', '/home/data/SP1314/raw/nb300/sp2013_326_57600.raw', '/home/data/SP1314/raw/nb300/sp2013_326_64800.raw', '/home/data/SP1314/raw/nb300/sp2013_326_72000.raw', '/home/data/SP1314/raw/nb300/sp2013_326_79200.raw', '/home/data/SP1314/raw/nb300/sp2013_327_00000.raw', '/home/data/SP1314/raw/nb300/sp2013_327_07200.raw', '/home/data/SP1314/raw/nb300/sp2013_327_14400.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 11 fixfile a_sp.gps frequency 300 gbin_style python gbindirbase /home/data/SP1314/gbin hcorr_inst ashtech help False hidedisplay True incremental True instname nb300 jitter 15 max_BLKprofiles 300 max_search_depth 300 maxrunsecs None min_filter_fraction 0.5 model nb 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 2013 progdir /home/currents/programs py_gbindirbase /home/data/SP1314/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_sp_refsm.asc sonar nb300 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 2013 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 2013-11-24 05:51:08,688 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:08,688 INFO quick_adcp step 1: set up editing files 2013-11-24 05:51:08,688 DEBUG quick_run executing commands from /home/data/SP1314/proc/nb300/edit 2013-11-24 05:51:08,688 DEBUG quick_run setup.m exists. not replacing 2013-11-24 05:51:08,688 DEBUG quick_run asetup.m exists. not replacing 2013-11-24 05:51:08,688 DEBUG quick_run aflagit_setup.m exists. not replacing 2013-11-24 05:51:08,688 DEBUG quick_subs dbname: ../adcpdb/a_sp 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 2013-11-24 05:51:08,689 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:08,689 INFO quick_adcp step 2: scan files for time range 2013-11-24 05:51:08,689 INFO quick_adcp about to run numpy scan, requiring python gbins 2013-11-24 05:51:08,689 DEBUG quick_npy Starting: scanping 2013-11-24 05:51:08,695 DEBUG quick_npy Ending: scanping 2013-11-24 05:51:08,696 DEBUG quick_subs start_end_time 2013/11/23 15:21:02 to 2013/11/23 15:49:12 2013-11-24 05:51:08,696 DEBUG quick_subs dd0: 326.639606 dd1: 326.659167 2013-11-24 05:51:08,696 INFO quick_adcp in quick_adcp.py: after scan; look for database times in /home/data/SP1314/proc/nb300 2013-11-24 05:51:08,696 INFO quick_adcp looking for database with adcpdb/a_sp*.blk 2013-11-24 05:51:08,697 INFO quick_adcp database found: listing blocks 2013-11-24 05:51:08,697 DEBUG quick_subs removing a_spdir.blk 2013-11-24 05:51:08,697 DEBUG quick_subs about to run mkblkdir 2013-11-24 05:51:08,697 DEBUG quick_subs database still exists; rerunning mkdirblk 2013-11-24 05:51:08,697 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2013-11-24 05:51:08,705 DEBUG quick_subs database passes. 2013-11-24 05:51:08,705 DEBUG quick_subs start_end_time 2013/11/23 15:23:02 to 2013/11/24 05:19:02 2013-11-24 05:51:08,705 DEBUG quick_subs dd0: 326.640995 dd1: 327.221551 2013-11-24 05:51:08,705 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2013-11-24 05:51:08,705 DEBUG quick_adcp origdb_time_range is 2013/11/23 15:23:02 to 2013/11/24 05:19:02 2013-11-24 05:51:08,705 DEBUG quick_adcp (326.640995 to 327.221551) 2013-11-24 05:51:08,705 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:08,705 INFO quick_adcp step 3: generate averaged data... 2013-11-24 05:51:08,706 DEBUG quick_run file load/ping_editparams.txt exists. not replacing 2013-11-24 05:51:08,706 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:08,706 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/load 2013-11-24 05:51:08,706 DEBUG quick_setup running python command "run_pingavg_npy" 2013-11-24 05:51:08,706 DEBUG quick_npy Starting: pingavg 2013-11-24 05:51:08,707 DEBUG quick_npy singleping editing parameters: 2013-11-24 05:51:08,707 DEBUG quick_npy bigtarget_mab_window : 11 2013-11-24 05:51:08,707 DEBUG quick_npy rl_endbin : 20 2013-11-24 05:51:08,708 DEBUG quick_npy max_search_depth : 300 2013-11-24 05:51:08,708 DEBUG quick_npy cor_cutoff : 120 2013-11-24 05:51:08,708 DEBUG quick_npy ampfilt : 40 2013-11-24 05:51:08,708 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2013-11-24 05:51:08,708 DEBUG quick_npy rl_startbin : 2 2013-11-24 05:51:08,708 DEBUG quick_npy ecutoff : 0.500000 2013-11-24 05:51:08,708 DEBUG quick_npy refavg_valcutoff : 1 2013-11-24 05:51:08,708 DEBUG quick_npy weakprof_percent : 30 2013-11-24 05:51:08,708 DEBUG quick_npy bigtarget_ampthresh : 55 2013-11-24 05:51:08,711 INFO pingavg Pingavg.run for time range 327.166610 to 327.242532 2013-11-24 05:51:08,715 DEBUG pingavg Chunk 1 of 1, 327.166610 to 327.242532 2013-11-24 05:51:08,715 DEBUG pingavg Nothing written 2013-11-24 05:51:08,716 DEBUG quick_npy wrote 0 averages 2013-11-24 05:51:08,716 DEBUG quick_npy Ending: pingavg 2013-11-24 05:51:08,716 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:08,716 INFO quick_adcp step 4: load averaged data (to database) 2013-11-24 05:51:08,717 DEBUG quick_subs in del_overlapping 2013-11-24 05:51:08,717 DEBUG quick_subs lastblock: 2013-11-24 05:51:08,717 DEBUG quick_subs 2 2013-11-24 05:51:08,717 DEBUG quick_subs lastcmd: 2013-11-24 05:51:08,717 DEBUG quick_subs 2 2013-11-24 05:51:08,717 DEBUG quick_subs delblks: 2013-11-24 05:51:08,717 DEBUG quick_subs [2] 2013-11-24 05:51:08,717 DEBUG quick_subs loadblks: 2013-11-24 05:51:08,717 DEBUG quick_subs [2] 2013-11-24 05:51:08,718 DEBUG quick_subs about to run mkblkdir 2013-11-24 05:51:08,718 DEBUG quick_subs database still exists; rerunning mkdirblk 2013-11-24 05:51:08,718 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2013-11-24 05:51:08,725 DEBUG quick_subs database passes. 2013-11-24 05:51:08,725 DEBUG quick_subs start_end_time 2013/11/23 15:23:02 to 2013/11/24 01:21:01 2013-11-24 05:51:08,725 DEBUG quick_subs dd0: 326.640995 dd1: 327.056262 2013-11-24 05:51:08,726 DEBUG quick_run [2] 2013-11-24 05:51:08,726 DEBUG quick_run cmdlist 2013-11-24 05:51:08,726 DEBUG quick_run ['./ens_blk002.cmd'] 2013-11-24 05:51:08,727 INFO quick_run Warning: 1 files will be loaded; 2 already exist 2013-11-24 05:51:08,727 INFO quick_run Sun Nov 24 05:51:08 2013 2013-11-24 05:51:08,727 INFO quick_run about to load uhdas files 2013-11-24 05:51:08,727 INFO quick_run /home/data/SP1314/raw/nb300/sp2013_326_55267.raw /home/data/SP1314/raw/nb300/sp2013_326_57600.raw /home/data/SP1314/raw/nb300/sp2013_326_64800.raw /home/data/SP1314/raw/nb300/sp2013_326_72000.raw /home/data/SP1314/raw/nb300/sp2013_326_79200.raw ... 2013-11-24 05:51:08,727 DEBUG quick_setup load/ldcodas.tmp exists 2013-11-24 05:51:08,727 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:08,727 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/load 2013-11-24 05:51:08,728 DEBUG quick_setup running python command "ldcodas" 2013-11-24 05:51:08,728 DEBUG quick_subs filling "thisload" timerange 2013-11-24 05:51:08,728 DEBUG quick_subs in ldcodas 2013-11-24 05:51:08,728 DEBUG quick_subs cmdlist: 2013-11-24 05:51:08,729 DEBUG quick_subs ['./ens_blk002.cmd'] 2013-11-24 05:51:08,729 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_sp DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2013 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk002.cmd 2013-11-24 05:51:08,729 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/ldcodas ldcodas.tmp 2013-11-24 05:51:08,747 DEBUG quick_subs removing a_spdir.blk 2013-11-24 05:51:08,747 DEBUG quick_subs about to run mkblkdir 2013-11-24 05:51:08,747 DEBUG quick_subs database still exists; rerunning mkdirblk 2013-11-24 05:51:08,747 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2013-11-24 05:51:08,754 DEBUG quick_subs database passes. 2013-11-24 05:51:08,755 DEBUG quick_subs start_end_time 2013/11/23 15:23:02 to 2013/11/24 05:49:02 2013-11-24 05:51:08,755 DEBUG quick_subs dd0: 326.640995 dd1: 327.242384 2013-11-24 05:51:08,755 INFO quick_adcp loaded_time_range is 2013/11/23 15:23:02 to 2013/11/24 05:49:02 2013-11-24 05:51:08,755 INFO quick_adcp (326.640995 to 327.242384) 2013-11-24 05:51:08,755 INFO quick_adcp origdb_time_range is 2013/11/23 15:23:02 to 2013/11/24 05:19:02 2013-11-24 05:51:08,755 INFO quick_adcp (326.640995 to 327.221551) 2013-11-24 05:51:08,755 INFO quick_adcp thisload_time_range is 2013/11/24 01:23:02 to 2013/11/24 05:49:02 2013-11-24 05:51:08,755 INFO quick_adcp (327.057662 to 327.057662) 2013-11-24 05:51:08,756 INFO quick_adcp --------------------- 2013-11-24 05:51:08,756 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:08,756 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/adcpdb 2013-11-24 05:51:08,756 DEBUG quick_setup running python command "lst_conf" 2013-11-24 05:51:08,756 DEBUG quick_subs dbname: a_sp output: a_sp.cnh time_ranges: all 2013-11-24 05:51:08,756 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_conf lst_conf.tmp 2013-11-24 05:51:08,770 DEBUG quick_setup found (in edit/asetup.m): 2013-11-24 05:51:08,770 DEBUG quick_setup config.beamangle is 30 2013-11-24 05:51:08,770 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:08,770 INFO quick_adcp step 5: set up files for gautoedit.py 2013-11-24 05:51:08,770 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2013-11-24 05:51:08,771 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:08,771 INFO quick_adcp step 6: set up files for gautoedit.py 2013-11-24 05:51:08,771 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:08,771 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/edit 2013-11-24 05:51:08,771 DEBUG quick_setup running python command "setflags" 2013-11-24 05:51:08,771 DEBUG quick_subs dbname: ../adcpdb/a_sp pg_min: 50 set_range_bit time_ranges: all 2013-11-24 05:51:08,771 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2013-11-24 05:51:08,778 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:08,778 INFO quick_adcp step 7: get navigation 2013-11-24 05:51:08,779 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:08,779 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/nav 2013-11-24 05:51:08,779 DEBUG quick_setup running python command "catnav" 2013-11-24 05:51:08,779 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2013-11-24 05:51:08,780 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:08,780 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/cal/rotate 2013-11-24 05:51:08,780 DEBUG quick_setup running python command "lst_hdg" 2013-11-24 05:51:08,780 DEBUG quick_subs dbname: ../../adcpdb/a_sp output: scn.hdg step_size= 1 year_base= 2013 time_ranges: all 2013-11-24 05:51:08,780 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_hdg lst_hdg.tmp 2013-11-24 05:51:08,786 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:08,786 INFO quick_adcp step 8: get heading correction 2013-11-24 05:51:08,787 DEBUG quick_run hcorr_inst is ashtech 2013-11-24 05:51:08,787 DEBUG quick_mpl Starting plot: hcorr 2013-11-24 05:51:08,792 DEBUG quick_mplplots found 0.601389 days of data 2013-11-24 05:51:08,792 DEBUG quick_mplplots figures with 4 panels per page, 1.000000 days per panel 2013-11-24 05:51:08,792 DEBUG quick_mplplots printing 1 pages 2013-11-24 05:51:09,059 DEBUG quick_mpl Ending plot: hcorr 2013-11-24 05:51:09,059 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:09,059 INFO quick_adcp step 9: rotate velocities 2013-11-24 05:51:09,059 DEBUG quick_setup cal/rotate/norotate.tmp exists 2013-11-24 05:51:09,059 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,059 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/cal/rotate 2013-11-24 05:51:09,060 DEBUG quick_setup running python command "norotate" 2013-11-24 05:51:09,060 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_sp LOG_FILE: rotate.log TIME_RANGE: 2013/11/23 15:23:02 to 2013/11/24 05:49:02 OPTION_LIST: water_and_bottom_track: year_base= 2013 /* time_angle_file: time_angle.ang */ amplitude= 1.0 angle_0= 0.0 end end 2013-11-24 05:51:09,060 DEBUG quick_setup about to run echo "writing dummy rotate file" 2013-11-24 05:51:09,064 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:09,064 INFO quick_adcp step 10: nav steps: run adcpsect 2013-11-24 05:51:09,064 DEBUG quick_setup nav/as_nav.tmp exists 2013-11-24 05:51:09,064 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,064 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/nav 2013-11-24 05:51:09,065 DEBUG quick_setup running python command "as_nav" 2013-11-24 05:51:09,065 DEBUG quick_subs dbname: ../adcpdb/a_sp output: a_sp step_size: 1 ndepth: 20 time_ranges: separate year_base= 2013 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 2013/11/23 15:23:02 to 2013/11/24 05:49:02 /* the whole time range */ 2013-11-24 05:51:09,065 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2013-11-24 05:51:09,074 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:09,074 INFO quick_adcp step 11: nav steps: run refabs 2013-11-24 05:51:09,074 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,075 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/nav 2013-11-24 05:51:09,075 DEBUG quick_setup running python command "refabs" 2013-11-24 05:51:09,075 DEBUG quick_subs fix_file_type: simple reference_file: a_sp.nav fix_file: a_sp.gps output: a_sp.ref year_base= 2013 ensemble_length= 300 gap_tolerance= 10 2013-11-24 05:51:09,075 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2013-11-24 05:51:09,085 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:09,086 INFO quick_adcp step 12: nav steps: run smoothr for plots 2013-11-24 05:51:09,086 DEBUG quick_setup nav/smoothr.tmp exists 2013-11-24 05:51:09,086 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,086 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/nav 2013-11-24 05:51:09,086 DEBUG quick_setup running python command "smoothr" 2013-11-24 05:51:09,087 DEBUG quick_subs reference_file: a_sp.nav refabs_output: a_sp.ref output: a_sp.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 2013-11-24 05:51:09,087 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2013-11-24 05:51:09,112 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:09,113 INFO quick_adcp step 13: nav steps: smooth navigation 2013-11-24 05:51:09,113 INFO quick_adcp about to run numpy refsm 2013-11-24 05:51:09,113 DEBUG quick_npy Starting: refsm 2013-11-24 05:51:09,128 DEBUG nav dtmin = -0.50 dtmax = 0.50 2013-11-24 05:51:09,167 DEBUG quick_npy Ending: refsm 2013-11-24 05:51:09,167 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:09,167 INFO quick_adcp step 14: nav steps: put smoothed nav into codasdb 2013-11-24 05:51:09,167 DEBUG quick_setup nav/putnav.tmp exists 2013-11-24 05:51:09,167 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,167 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/nav 2013-11-24 05:51:09,168 DEBUG quick_setup running python command "putnav" 2013-11-24 05:51:09,168 DEBUG quick_subs dbname: ../adcpdb/a_sp position_file: a_sp_refsm.asc year_base= 2013 tolerance= 5 navigation_sources: gps end 2013-11-24 05:51:09,168 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2013-11-24 05:51:09,178 INFO quick_adcp plotting navigation 2013-11-24 05:51:09,178 DEBUG quick_mpl Starting plot: nav 2013-11-24 05:51:09,444 DEBUG quick_mpl Ending plot: nav 2013-11-24 05:51:09,444 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:09,444 INFO quick_adcp step 15: nav steps: make reflayer plots 2013-11-24 05:51:09,445 DEBUG quick_mpl Starting plot: refl 2013-11-24 05:51:09,455 DEBUG quick_mplplots found 0.536103 days of data 2013-11-24 05:51:09,455 DEBUG quick_mplplots start day is 326.000000 2013-11-24 05:51:09,455 DEBUG quick_mplplots figures with 2.000000 days per page 2013-11-24 05:51:09,455 DEBUG quick_mplplots printing 1 pages 2013-11-24 05:51:09,455 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2013-11-24 05:51:09,725 DEBUG quick_mpl Ending plot: refl 2013-11-24 05:51:09,725 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:09,725 INFO quick_adcp step 16: find profile flags 2013-11-24 05:51:09,725 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,725 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/edit 2013-11-24 05:51:09,725 DEBUG quick_setup running python command "run_autoedit_npy" 2013-11-24 05:51:09,726 DEBUG quick_npy Starting: autoedit 2013-11-24 05:51:09,767 DEBUG pingedit wrote 1 bad bins to abadbin_tmp.asc 2013-11-24 05:51:09,786 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2013-11-24 05:51:09,786 DEBUG quick_npy Ending: autoedit 2013-11-24 05:51:09,786 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:09,786 INFO quick_adcp step 17: apply editing 2013-11-24 05:51:09,786 DEBUG quick_run starting in: /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,786 DEBUG quick_run executing commands from: edit 2013-11-24 05:51:09,787 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/dbupdate ../adcpdb/a_sp abadprf_tmp.asc 2013-11-24 05:51:09,793 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/badbin ../adcpdb/a_sp abadbin_tmp.asc 2013-11-24 05:51:09,798 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/set_lgb ../adcpdb/a_sp 30 2013-11-24 05:51:09,803 DEBUG quick_subs dbname: ../adcpdb/a_sp pg_min: 50 set_range_bit time_ranges: all 2013-11-24 05:51:09,803 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2013-11-24 05:51:09,811 DEBUG quick_run changing directories back to /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,812 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:09,812 INFO quick_adcp step 18: run nav steps 2013-11-24 05:51:09,812 DEBUG quick_setup nav/as_nav.tmp exists 2013-11-24 05:51:09,812 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,812 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/nav 2013-11-24 05:51:09,812 DEBUG quick_setup running python command "as_nav" 2013-11-24 05:51:09,812 DEBUG quick_subs dbname: ../adcpdb/a_sp output: a_sp step_size: 1 ndepth: 20 time_ranges: separate year_base= 2013 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 2013/11/23 15:23:02 to 2013/11/24 05:49:02 /* the whole time range */ 2013-11-24 05:51:09,812 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2013-11-24 05:51:09,822 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,822 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/nav 2013-11-24 05:51:09,823 DEBUG quick_setup running python command "refabs" 2013-11-24 05:51:09,823 DEBUG quick_subs fix_file_type: simple reference_file: a_sp.nav fix_file: a_sp.gps output: a_sp.ref year_base= 2013 ensemble_length= 300 gap_tolerance= 10 2013-11-24 05:51:09,823 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2013-11-24 05:51:09,831 DEBUG quick_setup nav/smoothr.tmp exists 2013-11-24 05:51:09,831 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,831 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/nav 2013-11-24 05:51:09,831 DEBUG quick_setup running python command "smoothr" 2013-11-24 05:51:09,831 DEBUG quick_subs reference_file: a_sp.nav refabs_output: a_sp.ref output: a_sp.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 2013-11-24 05:51:09,831 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2013-11-24 05:51:09,853 DEBUG quick_npy Starting: refsm 2013-11-24 05:51:09,869 DEBUG nav dtmin = -0.50 dtmax = 0.50 2013-11-24 05:51:09,887 DEBUG quick_npy Ending: refsm 2013-11-24 05:51:09,887 DEBUG quick_setup nav/putnav.tmp exists 2013-11-24 05:51:09,887 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:09,887 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/nav 2013-11-24 05:51:09,887 DEBUG quick_setup running python command "putnav" 2013-11-24 05:51:09,887 DEBUG quick_subs dbname: ../adcpdb/a_sp position_file: a_sp_refsm.asc year_base= 2013 tolerance= 5 navigation_sources: gps end 2013-11-24 05:51:09,888 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2013-11-24 05:51:09,898 DEBUG quick_mpl Starting plot: nav 2013-11-24 05:51:10,166 DEBUG quick_mpl Ending plot: nav 2013-11-24 05:51:10,167 DEBUG quick_mpl Starting plot: refl 2013-11-24 05:51:10,177 DEBUG quick_mplplots found 0.536103 days of data 2013-11-24 05:51:10,177 DEBUG quick_mplplots start day is 326.000000 2013-11-24 05:51:10,177 DEBUG quick_mplplots figures with 2.000000 days per page 2013-11-24 05:51:10,177 DEBUG quick_mplplots printing 1 pages 2013-11-24 05:51:10,177 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2013-11-24 05:51:10,449 DEBUG quick_mpl Ending plot: refl 2013-11-24 05:51:10,449 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:10,449 INFO quick_adcp step 19: plot temperature 2013-11-24 05:51:10,449 DEBUG quick_setup edit/lst_temp.tmp exists 2013-11-24 05:51:10,450 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:10,450 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/edit 2013-11-24 05:51:10,450 DEBUG quick_setup running python command "lst_temp" 2013-11-24 05:51:10,450 DEBUG quick_subs dbname: ../adcpdb/a_sp output: a_sp.tem step_size= 1 year_base= 2013 time_ranges: all 2013-11-24 05:51:10,450 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_temp lst_temp.tmp 2013-11-24 05:51:10,458 DEBUG quick_mpl Starting plot: temp 2013-11-24 05:51:10,463 DEBUG quick_mplplots plotting 434 points 2013-11-24 05:51:10,666 DEBUG quick_mpl Ending plot: temp 2013-11-24 05:51:10,666 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:10,666 INFO quick_adcp step 20: run calibration steps 2013-11-24 05:51:10,666 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2013-11-24 05:51:10,666 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:10,666 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/cal/botmtrk 2013-11-24 05:51:10,666 DEBUG quick_setup running python command "lst_btrk" 2013-11-24 05:51:10,666 DEBUG quick_subs dbname: ../../adcpdb/a_sp output: a_sp.btm step_size= 1 year_base= 2013 time_ranges: 2013/11/23 15:23:02 to 2013/11/24 05:49:02 /* whole time range */ 2013-11-24 05:51:10,667 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_btrk lst_btrk.tmp 2013-11-24 05:51:10,673 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2013-11-24 05:51:10,673 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:10,673 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/cal/botmtrk 2013-11-24 05:51:10,673 DEBUG quick_setup running python command "refabsbt" 2013-11-24 05:51:10,674 DEBUG quick_subs fix_file_type: simple reference_file: a_sp.btm fix_file: ../../nav/a_sp.gps output: a_sp.ref year_base= 2013 ensemble_length= 300 gap_tolerance= 60 2013-11-24 05:51:10,674 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabsbt refabsbt.tmp 2013-11-24 05:51:10,680 DEBUG quick_mpl Starting plot: btcal 2013-11-24 05:51:10,680 DEBUG quick_mplplots No data in a_sp.btm 2013-11-24 05:51:10,680 DEBUG quick_mplplots Returning from Btplot with no output 2013-11-24 05:51:10,680 DEBUG quick_mpl Ending plot: btcal 2013-11-24 05:51:10,681 DEBUG quick_setup nav/as_nav.tmp exists 2013-11-24 05:51:10,681 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:10,681 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/nav 2013-11-24 05:51:10,681 DEBUG quick_setup running python command "as_nav" 2013-11-24 05:51:10,681 DEBUG quick_subs dbname: ../adcpdb/a_sp output: a_sp step_size: 1 ndepth: 20 time_ranges: separate year_base= 2013 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 2013/11/23 15:23:02 to 2013/11/24 05:49:02 /* the whole time range */ 2013-11-24 05:51:10,681 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2013-11-24 05:51:10,691 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2013-11-24 05:51:10,691 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:10,691 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/cal/watertrk 2013-11-24 05:51:10,691 DEBUG quick_setup running python command "timslip" 2013-11-24 05:51:10,691 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_sp.gps reference_file: ../../nav/a_sp.nav output_file: a_sp_7.cal year_base= 2013 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 2013-11-24 05:51:10,692 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timslip timslip.tmp 2013-11-24 05:51:10,698 DEBUG quick_mpl Starting plot: wtcal 2013-11-24 05:51:10,700 DEBUG quick_mplplots Found 4 calibration points 2013-11-24 05:51:11,339 DEBUG quick_mpl Ending plot: wtcal 2013-11-24 05:51:11,340 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:11,340 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/cal/watertrk 2013-11-24 05:51:11,340 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2013-11-24 05:51:11,340 DEBUG quick_npy Starting: guess_xducerxy 2013-11-24 05:51:11,365 DEBUG quick_npy Ending: guess_xducerxy 2013-11-24 05:51:11,365 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:11,365 INFO quick_adcp step 21: extract matlab "allbins" 2013-11-24 05:51:11,365 DEBUG quick_asect ------------ step 18: make matlab files for plotting ------------- 2013-11-24 05:51:11,365 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:11,365 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/vector 2013-11-24 05:51:11,365 DEBUG quick_setup running python command "timegrid" 2013-11-24 05:51:11,365 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_sp.tmp 2013-11-24 05:51:11,373 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:11,373 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/vector 2013-11-24 05:51:11,373 DEBUG quick_setup running python command "as_vect" 2013-11-24 05:51:11,373 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_vect.tmp 2013-11-24 05:51:11,385 DEBUG quick_asect done making vector matfiles 2013-11-24 05:51:11,385 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:11,385 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/contour 2013-11-24 05:51:11,386 DEBUG quick_setup running python command "timegrid" 2013-11-24 05:51:11,386 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_sp.tmp 2013-11-24 05:51:11,393 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:11,393 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/contour 2013-11-24 05:51:11,393 DEBUG quick_setup running python command "as_cont" 2013-11-24 05:51:11,394 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_cont.tmp 2013-11-24 05:51:11,410 DEBUG quick_setup starting in /home/data/SP1314/proc/nb300 2013-11-24 05:51:11,410 DEBUG quick_setup executing commands from /home/data/SP1314/proc/nb300/contour 2013-11-24 05:51:11,410 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_sp 2013-11-24 05:51:11,442 DEBUG quick_asect done running getmat with "allbins" 2013-11-24 05:51:11,442 INFO quick_adcp --------------------------------------------- 2013-11-24 05:51:11,442 INFO quick_adcp step 22: write "cruise_info.txt" 2013-11-24 05:51:11,449 INFO root copying NOFIG to /home/adcp/www/figures/nb300_hcorr_plot.png 2013-11-24 05:51:11,450 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/nb300_hcorr_plot_thumb.png 2013-11-24 05:51:11,450 DEBUG root matfile is contour/contour_uv.mat 2013-11-24 05:51:11,450 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/nb300_cont_uv.mat 2013-11-24 05:51:11,450 DEBUG root matfile is vector/vector_uv.mat 2013-11-24 05:51:11,450 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/nb300_vect_uv.mat 2013-11-24 05:51:11,450 DEBUG root matfile is contour/contour_xy.mat 2013-11-24 05:51:11,451 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/nb300_cont_xy.mat 2013-11-24 05:51:11,451 DEBUG root matfile is vector/vector_xy.mat 2013-11-24 05:51:11,451 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/nb300_vect_xy.mat 2013-11-24 05:51:11,451 DEBUG root about to copy file edit/a_sp.tem to /home/adcp/www/data/nb300_temp.asc 2013-11-24 05:51:11,451 INFO root copying edit/a_sp.tem to /home/adcp/www/data/nb300_temp.asc 2013-11-24 05:51:11,518 DEBUG root about to copy netcdf file /home/data/SP1314/proc/nb300/contour/nb300.nc to /home/adcp/www/data/nb300.nc 2013-11-24 05:51:11,519 INFO root copying edit/a_sp.tem to /home/adcp/www/data/nb300.nc 2013-11-24 05:51:11,528 INFO root generating pingstats for nb300 2013-11-24 05:51:11,528 INFO root Ending quick_adcp.py