2011-09-02 16:06:45,547 DEBUG root about to write control file parameters to --yearbase 2011 --cruisename MGL1111 --configtype python --sonar os75bb --dbname a_mgl --datatype uhdas --cfgpath /home/data/MGL1111/proc/os75bb/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 2011-09-02 16:06:45,548 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d os75bb 2011-09-02 16:06:45,549 DEBUG quick_adcp progdir = /home/currents/programs 2011-09-02 16:06:45,549 DEBUG quick_adcp binos = lnx64 2011-09-02 16:06:45,551 DEBUG quick_setup found cruise_info.hcorr (seapath, hdg, 0) 2011-09-02 16:06:45,552 INFO quick_adcp importing numpy 2011-09-02 16:06:45,553 INFO quick_adcp importing matplotlib 2011-09-02 16:06:45,553 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 ddtime def_qlist del_overlapping fill_thisload_timerange get_asvars get_cmd_timerange get_filelist 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_loaddb run_loadping run_lstconfig run_lsttemp run_matbincmd run_matfiles run_pingavg_npy run_plotter run_putnav run_py_codaseditsetup run_py_findpflags run_py_pingeditsetup run_pybincmd run_pygbin_npy run_refabs run_refplots run_refsm run_refsm_npy run_rotate run_scanbin_npy run_scandata run_scanping_npy run_setflags run_smoothr run_updategbin run_updatepygbin run_xducerxy scanping setflags smoothr timegrid timslip ubprint user_defined_headfunc write_codas_editdefaults write_ping_editdefaults write_timerange_file zapsetup 2011-09-02 16:06:45,553 DEBUG quick_adcp cwd is /data/MGL1111/proc/os75bb 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 2011-09-02 16:06:45,554 DEBUG quick_adcp original fix file is a_mgl.gps 2011-09-02 16:06:45,554 DEBUG quick_adcp smoothed nav file is a_mgl_refsm.asc 2011-09-02 16:06:45,554 DEBUG quick_asect extracting matlab files for os75, bb pings 2011-09-02 16:06:45,573 DEBUG quick_subs found 304 files using wildcard expansion from "/home/data/MGL1111/raw/os75/*.raw" 2011-09-02 16:06:45,573 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/MGL1111/raw/os75/mgl2011_219_77635.raw ... 2011-09-02 16:06:45,574 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/MGL1111/raw/os75/mgl2011_219_77635.raw ... 2011-09-02 16:06:45,575 DEBUG quick_adcp Fri Sep 2 16:06:45 2011 running quick_adcp.py as follows: --cntfile /home/data/MGL1111/proc/os75bb/os75bb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_mgl 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 23 gridnum 80 increment 10 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2011 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 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/MGL1111/proc/os75bb/config cntfile /home/data/MGL1111/proc/os75bb/os75bb_qpy.cnt 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'/home/data/MGL1111/raw/os75/mgl2011_244_14400.raw', '/home/data/MGL1111/raw/os75/mgl2011_244_21600.raw', '/home/data/MGL1111/raw/os75/mgl2011_244_28800.raw', '/home/data/MGL1111/raw/os75/mgl2011_244_36000.raw', '/home/data/MGL1111/raw/os75/mgl2011_244_43200.raw', '/home/data/MGL1111/raw/os75/mgl2011_244_50400.raw', '/home/data/MGL1111/raw/os75/mgl2011_244_57600.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 23 fixfile a_mgl.gps frequency 75 gbin_style python gbindirbase /home/data/MGL1111/gbin hcorr_inst seapath help False hidedisplay True incremental True instname os75 jitter 15 max_BLKprofiles 399 max_search_depth 1500 maxrunsecs None min_filter_fraction 0.5 model os nosave_editcfg 0 num_persistence 24 numbins 128 orig_fixfile a_mgl.gps overview False pgmin 50 ping_headcorr False pingtype bb post_headcorr None printformats png proc_engine python proc_yearbase 2011 progdir /home/currents/programs py_gbindirbase /home/data/MGL1111/gbin quiet False 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_mgl_refsm.asc sonar os75bb 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 False xducer_dy False yearbase 2011 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 2011-09-02 16:06:45,576 DEBUG quick_run ------------ step 3 (create suitable setup files for editing) ------------- 2011-09-02 16:06:45,576 DEBUG quick_run executing commands from /data/MGL1111/proc/os75bb/edit 2011-09-02 16:06:45,576 DEBUG quick_run setup.m exists. not replacing 2011-09-02 16:06:45,576 DEBUG quick_run asetup.m exists. not replacing 2011-09-02 16:06:45,576 DEBUG quick_run aflagit_setup.m exists. not replacing 2011-09-02 16:06:45,576 DEBUG quick_adcp about to run numpy scan, requiring python gbins 2011-09-02 16:06:45,576 DEBUG quick_npy Starting: scanping 2011-09-02 16:06:46,008 DEBUG quick_npy Ending: scanping 2011-09-02 16:06:46,009 DEBUG quick_subs start_end_time 2011/08/08 21:33:59 to 2011/08/08 21:59:15 2011-09-02 16:06:46,009 DEBUG quick_subs dd0: 219.898600 dd1: 219.916146 2011-09-02 16:06:46,009 DEBUG quick_adcp in quick_adcp.py: after scan; look for database times in /data/MGL1111/proc/os75bb 2011-09-02 16:06:46,010 DEBUG quick_adcp looking for database with adcpdb/a_mgl*.blk 2011-09-02 16:06:46,010 DEBUG quick_adcp database found: listing blocks 2011-09-02 16:06:46,010 DEBUG quick_subs removing a_mgldir.blk 2011-09-02 16:06:46,011 DEBUG quick_subs about to run mkblkdir 2011-09-02 16:06:46,011 DEBUG quick_subs database still exists; rerunning mkdirblk 2011-09-02 16:06:46,011 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2011-09-02 16:06:46,023 DEBUG quick_subs database passes. 2011-09-02 16:06:46,023 DEBUG quick_subs start_end_time 2011/08/08 21:38:59 to 2011/09/02 15:31:45 2011-09-02 16:06:46,023 DEBUG quick_subs dd0: 219.902072 dd1: 244.647049 2011-09-02 16:06:46,024 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2011-09-02 16:06:46,024 DEBUG quick_adcp origdb_time_range is 2011/08/08 21:38:59 to 2011/09/02 15:31:45 2011-09-02 16:06:46,024 DEBUG quick_adcp (219.902072 to 244.647049) 2011-09-02 16:06:46,024 DEBUG quick_run file load/ping_editparams.txt exists. not replacing 2011-09-02 16:06:46,024 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:46,024 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/load 2011-09-02 16:06:46,025 DEBUG quick_setup running python command "run_pingavg_npy" 2011-09-02 16:06:46,025 DEBUG quick_npy Starting: pingavg 2011-09-02 16:06:46,027 DEBUG quick_npy singleping editing parameters: 2011-09-02 16:06:46,027 DEBUG quick_npy bigtarget_mab_window : 11 2011-09-02 16:06:46,027 DEBUG quick_npy rl_endbin : 20 2011-09-02 16:06:46,027 DEBUG quick_npy max_search_depth : 1500 2011-09-02 16:06:46,027 DEBUG quick_npy cor_cutoff : 120 2011-09-02 16:06:46,028 DEBUG quick_npy ampfilt : 40 2011-09-02 16:06:46,028 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2011-09-02 16:06:46,028 DEBUG quick_npy rl_startbin : 2 2011-09-02 16:06:46,028 DEBUG quick_npy ecutoff : 1 2011-09-02 16:06:46,028 DEBUG quick_npy refavg_valcutoff : 1 2011-09-02 16:06:46,028 DEBUG quick_npy weakprof_percent : 30 2011-09-02 16:06:46,028 DEBUG quick_npy bigtarget_ampthresh : 55 2011-09-02 16:06:46,041 INFO pingavg Pingavg.run for time range 244.666692 to 244.668069 2011-09-02 16:06:46,069 DEBUG pingavg Chunk 1 of 1, 244.666692 to 244.668069 2011-09-02 16:06:46,070 DEBUG pingavg Nothing written 2011-09-02 16:06:46,070 DEBUG quick_npy wrote 0 averages 2011-09-02 16:06:46,070 DEBUG quick_npy Ending: pingavg 2011-09-02 16:06:46,071 DEBUG quick_subs in del_overlapping 2011-09-02 16:06:46,071 DEBUG quick_subs lastblock: 2011-09-02 16:06:46,071 DEBUG quick_subs 38 2011-09-02 16:06:46,071 DEBUG quick_subs lastcmd: 2011-09-02 16:06:46,071 DEBUG quick_subs 38 2011-09-02 16:06:46,072 DEBUG quick_subs delblks: 2011-09-02 16:06:46,072 DEBUG quick_subs [38] 2011-09-02 16:06:46,072 DEBUG quick_subs loadblks: 2011-09-02 16:06:46,072 DEBUG quick_subs [38] 2011-09-02 16:06:46,073 DEBUG quick_subs about to run mkblkdir 2011-09-02 16:06:46,073 DEBUG quick_subs database still exists; rerunning mkdirblk 2011-09-02 16:06:46,073 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2011-09-02 16:06:46,084 DEBUG quick_subs database passes. 2011-09-02 16:06:46,084 DEBUG quick_subs start_end_time 2011/08/08 21:38:59 to 2011/09/02 10:36:46 2011-09-02 16:06:46,084 DEBUG quick_subs dd0: 219.902072 dd1: 244.442199 2011-09-02 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/home/data/MGL1111/raw/os75/mgl2011_238_85452.raw /home/data/MGL1111/raw/os75/mgl2011_239_00000.raw /home/data/MGL1111/raw/os75/mgl2011_239_08249.raw /home/data/MGL1111/raw/os75/mgl2011_239_15326.raw /home/data/MGL1111/raw/os75/mgl2011_239_21600.raw /home/data/MGL1111/raw/os75/mgl2011_239_28614.raw /home/data/MGL1111/raw/os75/mgl2011_239_28800.raw /home/data/MGL1111/raw/os75/mgl2011_239_36000.raw /home/data/MGL1111/raw/os75/mgl2011_239_43200.raw /home/data/MGL1111/raw/os75/mgl2011_239_50400.raw /home/data/MGL1111/raw/os75/mgl2011_239_57600.raw /home/data/MGL1111/raw/os75/mgl2011_239_67279.raw /home/data/MGL1111/raw/os75/mgl2011_239_72000.raw /home/data/MGL1111/raw/os75/mgl2011_239_79274.raw /home/data/MGL1111/raw/os75/mgl2011_240_03665.raw /home/data/MGL1111/raw/os75/mgl2011_240_07200.raw /home/data/MGL1111/raw/os75/mgl2011_240_14275.raw /home/data/MGL1111/raw/os75/mgl2011_240_14400.raw /home/data/MGL1111/raw/os75/mgl2011_240_23804.raw /home/data/MGL1111/raw/os75/mgl2011_240_28800.raw /home/data/MGL1111/raw/os75/mgl2011_240_36000.raw /home/data/MGL1111/raw/os75/mgl2011_240_43200.raw /home/data/MGL1111/raw/os75/mgl2011_240_50400.raw /home/data/MGL1111/raw/os75/mgl2011_240_57600.raw /home/data/MGL1111/raw/os75/mgl2011_240_64800.raw /home/data/MGL1111/raw/os75/mgl2011_240_72000.raw /home/data/MGL1111/raw/os75/mgl2011_240_79200.raw /home/data/MGL1111/raw/os75/mgl2011_241_00000.raw /home/data/MGL1111/raw/os75/mgl2011_241_07200.raw /home/data/MGL1111/raw/os75/mgl2011_241_14400.raw /home/data/MGL1111/raw/os75/mgl2011_241_21600.raw /home/data/MGL1111/raw/os75/mgl2011_241_28800.raw /home/data/MGL1111/raw/os75/mgl2011_241_36000.raw /home/data/MGL1111/raw/os75/mgl2011_241_43200.raw /home/data/MGL1111/raw/os75/mgl2011_241_50400.raw /home/data/MGL1111/raw/os75/mgl2011_241_57600.raw /home/data/MGL1111/raw/os75/mgl2011_241_64800.raw /home/data/MGL1111/raw/os75/mgl2011_241_72000.raw /home/data/MGL1111/raw/os75/mgl2011_241_79200.raw /home/data/MGL1111/raw/os75/mgl2011_242_00000.raw /home/data/MGL1111/raw/os75/mgl2011_242_07200.raw /home/data/MGL1111/raw/os75/mgl2011_242_14400.raw /home/data/MGL1111/raw/os75/mgl2011_242_21600.raw /home/data/MGL1111/raw/os75/mgl2011_242_28800.raw /home/data/MGL1111/raw/os75/mgl2011_242_36000.raw /home/data/MGL1111/raw/os75/mgl2011_242_43200.raw /home/data/MGL1111/raw/os75/mgl2011_242_50400.raw /home/data/MGL1111/raw/os75/mgl2011_242_57600.raw /home/data/MGL1111/raw/os75/mgl2011_242_64800.raw /home/data/MGL1111/raw/os75/mgl2011_242_72000.raw /home/data/MGL1111/raw/os75/mgl2011_242_79200.raw /home/data/MGL1111/raw/os75/mgl2011_243_00000.raw /home/data/MGL1111/raw/os75/mgl2011_243_07200.raw /home/data/MGL1111/raw/os75/mgl2011_243_14400.raw /home/data/MGL1111/raw/os75/mgl2011_243_21600.raw /home/data/MGL1111/raw/os75/mgl2011_243_28800.raw /home/data/MGL1111/raw/os75/mgl2011_243_36000.raw /home/data/MGL1111/raw/os75/mgl2011_243_43200.raw /home/data/MGL1111/raw/os75/mgl2011_243_50400.raw /home/data/MGL1111/raw/os75/mgl2011_243_57600.raw /home/data/MGL1111/raw/os75/mgl2011_243_64800.raw /home/data/MGL1111/raw/os75/mgl2011_243_72000.raw /home/data/MGL1111/raw/os75/mgl2011_243_79200.raw /home/data/MGL1111/raw/os75/mgl2011_244_00000.raw /home/data/MGL1111/raw/os75/mgl2011_244_07200.raw /home/data/MGL1111/raw/os75/mgl2011_244_14400.raw /home/data/MGL1111/raw/os75/mgl2011_244_21600.raw /home/data/MGL1111/raw/os75/mgl2011_244_28800.raw /home/data/MGL1111/raw/os75/mgl2011_244_36000.raw /home/data/MGL1111/raw/os75/mgl2011_244_43200.raw /home/data/MGL1111/raw/os75/mgl2011_244_50400.raw /home/data/MGL1111/raw/os75/mgl2011_244_57600.raw 2011-09-02 16:06:46,087 DEBUG quick_setup load/ldcodas.tmp exists 2011-09-02 16:06:46,087 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:46,088 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/load 2011-09-02 16:06:46,088 DEBUG quick_setup running python command "ldcodas" 2011-09-02 16:06:46,088 DEBUG quick_subs filling "thisload" timerange 2011-09-02 16:06:46,089 DEBUG quick_subs in ldcodas 2011-09-02 16:06:46,089 DEBUG quick_subs cmdlist: 2011-09-02 16:06:46,089 DEBUG quick_subs ['./ens_blk038.cmd'] 2011-09-02 16:06:46,089 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_mgl DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2011 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk038.cmd 2011-09-02 16:06:46,089 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/ldcodas ldcodas.tmp 2011-09-02 16:06:46,107 DEBUG quick_subs removing a_mgldir.blk 2011-09-02 16:06:46,107 DEBUG quick_subs about to run mkblkdir 2011-09-02 16:06:46,108 DEBUG quick_subs database still exists; rerunning mkdirblk 2011-09-02 16:06:46,108 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2011-09-02 16:06:46,120 DEBUG quick_subs database passes. 2011-09-02 16:06:46,121 DEBUG quick_subs start_end_time 2011/08/08 21:38:59 to 2011/09/02 16:01:45 2011-09-02 16:06:46,121 DEBUG quick_subs dd0: 219.902072 dd1: 244.667882 2011-09-02 16:06:46,121 INFO quick_adcp --------------------- 2011-09-02 16:06:46,122 INFO quick_adcp loaded_time_range is 2011/08/08 21:38:59 to 2011/09/02 16:01:45 2011-09-02 16:06:46,122 INFO quick_adcp (219.902072 to 244.667882) 2011-09-02 16:06:46,122 INFO quick_adcp origdb_time_range is 2011/08/08 21:38:59 to 2011/09/02 15:31:45 2011-09-02 16:06:46,122 INFO quick_adcp (219.902072 to 244.647049) 2011-09-02 16:06:46,122 INFO quick_adcp thisload_time_range is 2011/09/02 10:41:46 to 2011/09/02 16:01:45 2011-09-02 16:06:46,122 INFO quick_adcp (244.445671 to 244.445671) 2011-09-02 16:06:46,123 INFO quick_adcp --------------------- 2011-09-02 16:06:46,123 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:46,123 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/adcpdb 2011-09-02 16:06:46,123 DEBUG quick_setup running python command "lst_conf" 2011-09-02 16:06:46,123 DEBUG quick_subs dbname: a_mgl output: a_mgl.cnh time_ranges: all 2011-09-02 16:06:46,124 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_conf lst_conf.tmp 2011-09-02 16:06:46,864 DEBUG quick_setup found (in edit/asetup.m): 2011-09-02 16:06:46,865 DEBUG quick_setup config.beamangle is 30 2011-09-02 16:06:46,865 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2011-09-02 16:06:46,865 DEBUG quick_run ------------ step 4: run setflags ------------- 2011-09-02 16:06:46,865 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:46,865 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/edit 2011-09-02 16:06:46,865 DEBUG quick_setup running python command "setflags" 2011-09-02 16:06:46,865 DEBUG quick_subs dbname: ../adcpdb/a_mgl pg_min: 50 set_range_bit time_ranges: all 2011-09-02 16:06:46,865 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2011-09-02 16:06:46,923 DEBUG quick_run ------------ step 5: get fixes from load/*.gps2 files ------------- 2011-09-02 16:06:46,923 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:46,923 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/nav 2011-09-02 16:06:46,923 DEBUG quick_setup running python command "catnav" 2011-09-02 16:06:46,927 DEBUG quick_run ------------ step 6: get heading correction (if applicable) ------------- 2011-09-02 16:06:46,927 DEBUG quick_run hcorr_inst is seapath 2011-09-02 16:06:46,927 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2011-09-02 16:06:46,927 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:46,927 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/cal/rotate 2011-09-02 16:06:46,927 DEBUG quick_setup running python command "lst_hdg" 2011-09-02 16:06:46,927 DEBUG quick_subs dbname: ../../adcpdb/a_mgl output: scn.hdg step_size= 1 year_base= 2011 time_ranges: all 2011-09-02 16:06:46,928 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_hdg lst_hdg.tmp 2011-09-02 16:06:46,970 DEBUG quick_mpl Starting plot: hcorr 2011-09-02 16:06:47,052 DEBUG quick_mplplots found 24.765810 days of data 2011-09-02 16:06:47,053 DEBUG quick_mplplots figures with 4 panels per page, 1.000000 days per panel 2011-09-02 16:06:47,053 DEBUG quick_mplplots printing 7 pages 2011-09-02 16:06:47,744 DEBUG quick_mpl Ending plot: hcorr 2011-09-02 16:06:47,744 DEBUG quick_run ------------ step 7: rotate ------------- 2011-09-02 16:06:47,744 DEBUG quick_setup cal/rotate/norotate.tmp exists 2011-09-02 16:06:47,745 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:47,745 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/cal/rotate 2011-09-02 16:06:47,745 DEBUG quick_setup running python command "norotate" 2011-09-02 16:06:47,745 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_mgl LOG_FILE: rotate.log TIME_RANGE: 2011/08/08 21:38:59 to 2011/09/02 16:01:45 OPTION_LIST: water_and_bottom_track: year_base= 2011 /* time_angle_file: time_angle.ang */ amplitude= 1.0 angle_0= 0.0 end end 2011-09-02 16:06:47,745 DEBUG quick_setup about to run echo "writing dummy rotate file" 2011-09-02 16:06:47,749 DEBUG quick_run ------------ step 8: run adcpsect (for calib) ------------- 2011-09-02 16:06:47,749 DEBUG quick_setup nav/as_nav.tmp exists 2011-09-02 16:06:47,750 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:47,750 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/nav 2011-09-02 16:06:47,750 DEBUG quick_setup running python command "as_nav" 2011-09-02 16:06:47,750 DEBUG quick_subs dbname: ../adcpdb/a_mgl output: a_mgl step_size: 1 ndepth: 20 time_ranges: separate year_base= 2011 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 2011/08/08 21:38:59 to 2011/09/02 16:01:45 /* the whole time range */ 2011-09-02 16:06:47,750 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2011-09-02 16:06:47,826 DEBUG quick_run ------------ step 9: run refabs (for calib) ------------- 2011-09-02 16:06:47,826 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:47,826 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/nav 2011-09-02 16:06:47,826 DEBUG quick_setup running python command "refabs" 2011-09-02 16:06:47,826 DEBUG quick_subs fix_file_type: simple reference_file: a_mgl.nav fix_file: a_mgl.gps output: a_mgl.ref year_base= 2011 ensemble_length= 300 gap_tolerance= 10 2011-09-02 16:06:47,826 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2011-09-02 16:06:47,890 DEBUG quick_run ------------ step 10: get smoothed navigation (for calib) ------------- 2011-09-02 16:06:47,890 DEBUG quick_setup nav/smoothr.tmp exists 2011-09-02 16:06:47,890 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:47,890 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/nav 2011-09-02 16:06:47,890 DEBUG quick_setup running python command "smoothr" 2011-09-02 16:06:47,890 DEBUG quick_subs reference_file: a_mgl.nav refabs_output: a_mgl.ref output: a_mgl.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 2011-09-02 16:06:47,891 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2011-09-02 16:06:48,205 DEBUG quick_adcp about to run numpy refsm 2011-09-02 16:06:48,225 DEBUG quick_npy Starting: refsm 2011-09-02 16:06:48,447 INFO nav dtmin = -0.50 dtmax = 4.56 2011-09-02 16:06:48,705 DEBUG quick_npy Ending: refsm 2011-09-02 16:06:48,705 DEBUG quick_run ------------ step 11: put smoothed navigation back into database ------------- 2011-09-02 16:06:48,705 DEBUG quick_setup nav/putnav.tmp exists 2011-09-02 16:06:48,705 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:48,705 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/nav 2011-09-02 16:06:48,705 DEBUG quick_setup running python command "putnav" 2011-09-02 16:06:48,705 DEBUG quick_subs dbname: ../adcpdb/a_mgl position_file: a_mgl_refsm.asc year_base= 2011 tolerance= 5 navigation_sources: gps end 2011-09-02 16:06:48,706 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2011-09-02 16:06:50,922 DEBUG quick_adcp plotting navigation 2011-09-02 16:06:50,922 DEBUG quick_mpl Starting plot: nav 2011-09-02 16:06:51,319 DEBUG quick_mpl Ending plot: nav 2011-09-02 16:06:51,319 DEBUG quick_mpl Starting plot: refl 2011-09-02 16:06:51,511 DEBUG quick_mplplots found 24.758874 days of data 2011-09-02 16:06:51,511 DEBUG quick_mplplots start day is 219.000000 2011-09-02 16:06:51,511 DEBUG quick_mplplots figures with 2.000000 days per page 2011-09-02 16:06:51,511 DEBUG quick_mplplots printing 13 pages 2011-09-02 16:06:51,512 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2011-09-02 16:06:51,512 INFO quick_mplplots startdd is 219.0 2011-09-02 16:06:51,512 INFO quick_mplplots dt is 2.0 2011-09-02 16:06:52,192 DEBUG quick_mpl Ending plot: refl 2011-09-02 16:06:52,192 DEBUG quick_run ------------ step 13: automatically find profile flags using python ------------- 2011-09-02 16:06:52,192 DEBUG quick_run find profile flags ------------ *** ------------- 2011-09-02 16:06:52,192 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:52,192 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/edit 2011-09-02 16:06:52,192 DEBUG quick_setup running python command "run_autoedit_npy" 2011-09-02 16:06:52,192 DEBUG quick_npy Starting: autoedit 2011-09-02 16:06:52,467 DEBUG quick_npy Ending: autoedit 2011-09-02 16:06:52,467 DEBUG quick_run ------------ step 14: apply all profile flags to database ------------- 2011-09-02 16:06:52,467 DEBUG quick_run starting in: /data/MGL1111/proc/os75bb 2011-09-02 16:06:52,467 DEBUG quick_run executing commands from: edit 2011-09-02 16:06:52,469 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/badbin ../adcpdb/a_mgl abadbin_tmp.asc 2011-09-02 16:06:52,477 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/set_lgb ../adcpdb/a_mgl 30 2011-09-02 16:06:52,483 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2011-09-02 16:06:52,537 DEBUG quick_run changing directories back to /data/MGL1111/proc/os75bb 2011-09-02 16:06:52,537 DEBUG quick_adcp step 15: rerun nav steps, redo reflayer plots 2011-09-02 16:06:52,537 DEBUG quick_run ------------ step 8: run adcpsect (for calib) ------------- 2011-09-02 16:06:52,537 DEBUG quick_setup nav/as_nav.tmp exists 2011-09-02 16:06:52,537 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:52,537 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/nav 2011-09-02 16:06:52,538 DEBUG quick_setup running python command "as_nav" 2011-09-02 16:06:52,538 DEBUG quick_subs dbname: ../adcpdb/a_mgl output: a_mgl step_size: 1 ndepth: 20 time_ranges: separate year_base= 2011 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 2011/08/08 21:38:59 to 2011/09/02 16:01:45 /* the whole time range */ 2011-09-02 16:06:52,538 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2011-09-02 16:06:52,611 DEBUG quick_run ------------ step 9: run refabs (for calib) ------------- 2011-09-02 16:06:52,611 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:52,611 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/nav 2011-09-02 16:06:52,611 DEBUG quick_setup running python command "refabs" 2011-09-02 16:06:52,611 DEBUG quick_subs fix_file_type: simple reference_file: a_mgl.nav fix_file: a_mgl.gps output: a_mgl.ref year_base= 2011 ensemble_length= 300 gap_tolerance= 10 2011-09-02 16:06:52,612 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2011-09-02 16:06:52,675 DEBUG quick_run ------------ step 10: get smoothed navigation (for calib) ------------- 2011-09-02 16:06:52,676 DEBUG quick_setup nav/smoothr.tmp exists 2011-09-02 16:06:52,676 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:52,676 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/nav 2011-09-02 16:06:52,676 DEBUG quick_setup running python command "smoothr" 2011-09-02 16:06:52,676 DEBUG quick_subs reference_file: a_mgl.nav refabs_output: a_mgl.ref output: a_mgl.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 2011-09-02 16:06:52,676 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2011-09-02 16:06:52,983 DEBUG quick_adcp running refsm 2011-09-02 16:06:53,076 DEBUG quick_npy Starting: refsm 2011-09-02 16:06:53,291 INFO nav dtmin = -0.50 dtmax = 4.56 2011-09-02 16:06:53,542 DEBUG quick_npy Ending: refsm 2011-09-02 16:06:53,542 DEBUG quick_run ------------ step 11: put smoothed navigation back into database ------------- 2011-09-02 16:06:53,543 DEBUG quick_setup nav/putnav.tmp exists 2011-09-02 16:06:53,543 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:53,543 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/nav 2011-09-02 16:06:53,543 DEBUG quick_setup running python command "putnav" 2011-09-02 16:06:53,543 DEBUG quick_subs dbname: ../adcpdb/a_mgl position_file: a_mgl_refsm.asc year_base= 2011 tolerance= 5 navigation_sources: gps end 2011-09-02 16:06:53,543 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2011-09-02 16:06:56,156 DEBUG quick_mpl Starting plot: nav 2011-09-02 16:06:56,556 DEBUG quick_mpl Ending plot: nav 2011-09-02 16:06:56,557 DEBUG quick_mpl Starting plot: refl 2011-09-02 16:06:56,749 DEBUG quick_mplplots found 24.758874 days of data 2011-09-02 16:06:56,750 DEBUG quick_mplplots start day is 219.000000 2011-09-02 16:06:56,750 DEBUG quick_mplplots figures with 2.000000 days per page 2011-09-02 16:06:56,750 DEBUG quick_mplplots printing 13 pages 2011-09-02 16:06:56,750 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2011-09-02 16:06:56,750 INFO quick_mplplots startdd is 219.0 2011-09-02 16:06:56,750 INFO quick_mplplots dt is 2.0 2011-09-02 16:06:57,440 DEBUG quick_mpl Ending plot: refl 2011-09-02 16:06:57,441 DEBUG quick_run ------------ step 16: list temperature and plot it ------------- 2011-09-02 16:06:57,441 DEBUG quick_setup edit/lst_temp.tmp exists 2011-09-02 16:06:57,441 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:57,441 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/edit 2011-09-02 16:06:57,441 DEBUG quick_setup running python command "lst_temp" 2011-09-02 16:06:57,441 DEBUG quick_subs dbname: ../adcpdb/a_mgl output: a_mgl.tem step_size= 1 year_base= 2011 time_ranges: all 2011-09-02 16:06:57,442 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_temp lst_temp.tmp 2011-09-02 16:06:57,490 DEBUG quick_mpl Starting plot: temp 2011-09-02 16:06:57,555 DEBUG quick_mplplots plotting 6793 points 2011-09-02 16:06:57,837 DEBUG quick_mpl Ending plot: temp 2011-09-02 16:06:57,838 DEBUG quick_run ------------ step 17: bottom track and watertrack calibrations ------------- 2011-09-02 16:06:57,838 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2011-09-02 16:06:57,838 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:57,838 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/cal/botmtrk 2011-09-02 16:06:57,838 DEBUG quick_setup running python command "lst_btrk" 2011-09-02 16:06:57,838 DEBUG quick_subs dbname: ../../adcpdb/a_mgl output: a_mgl.btm step_size= 1 year_base= 2011 time_ranges: 2011/08/08 21:38:59 to 2011/09/02 16:01:45 /* whole time range */ 2011-09-02 16:06:57,838 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_btrk lst_btrk.tmp 2011-09-02 16:06:57,856 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2011-09-02 16:06:57,857 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:57,857 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/cal/botmtrk 2011-09-02 16:06:57,857 DEBUG quick_setup running python command "refabsbt" 2011-09-02 16:06:57,857 DEBUG quick_subs fix_file_type: simple reference_file: a_mgl.btm fix_file: ../../nav/a_mgl.gps output: a_mgl.ref year_base= 2011 ensemble_length= 300 gap_tolerance= 60 2011-09-02 16:06:57,857 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabsbt refabsbt.tmp 2011-09-02 16:06:57,863 DEBUG quick_mpl Starting plot: btcal 2011-09-02 16:06:57,863 DEBUG quick_mplplots No data in a_mgl.btm 2011-09-02 16:06:57,863 DEBUG quick_mplplots Returning from Btplot with no output 2011-09-02 16:06:57,864 DEBUG quick_mpl Ending plot: btcal 2011-09-02 16:06:57,864 DEBUG quick_setup nav/as_nav.tmp exists 2011-09-02 16:06:57,864 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:57,864 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/nav 2011-09-02 16:06:57,864 DEBUG quick_setup running python command "as_nav" 2011-09-02 16:06:57,864 DEBUG quick_subs dbname: ../adcpdb/a_mgl output: a_mgl step_size: 1 ndepth: 20 time_ranges: separate year_base= 2011 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 2011/08/08 21:38:59 to 2011/09/02 16:01:45 /* the whole time range */ 2011-09-02 16:06:57,864 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2011-09-02 16:06:57,940 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2011-09-02 16:06:57,941 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:57,941 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/cal/watertrk 2011-09-02 16:06:57,941 DEBUG quick_setup running python command "timslip" 2011-09-02 16:06:57,941 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_mgl.gps reference_file: ../../nav/a_mgl.nav output_file: a_mgl_7.cal year_base= 2011 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 2011-09-02 16:06:57,941 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timslip timslip.tmp 2011-09-02 16:06:57,968 DEBUG quick_mpl Starting plot: wtcal 2011-09-02 16:06:57,971 DEBUG quick_mplplots Found 63 calibration points 2011-09-02 16:06:58,771 DEBUG quick_mpl Ending plot: wtcal 2011-09-02 16:06:59,366 DEBUG quick_asect ------------ step 18: make matlab files for plotting ------------- 2011-09-02 16:06:59,366 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:06:59,366 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/vector 2011-09-02 16:06:59,366 DEBUG quick_setup running python command "timegrid" 2011-09-02 16:06:59,367 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_mgl.tmp 2011-09-02 16:07:00,000 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:07:00,000 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/vector 2011-09-02 16:07:00,000 DEBUG quick_setup running python command "as_vect" 2011-09-02 16:07:00,001 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_vect.tmp 2011-09-02 16:07:00,124 DEBUG quick_asect done making vector matfiles 2011-09-02 16:07:00,125 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:07:00,125 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/contour 2011-09-02 16:07:00,125 DEBUG quick_setup running python command "timegrid" 2011-09-02 16:07:00,125 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_mgl.tmp 2011-09-02 16:07:00,138 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:07:00,138 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/contour 2011-09-02 16:07:00,138 DEBUG quick_setup running python command "as_cont" 2011-09-02 16:07:00,139 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_cont.tmp 2011-09-02 16:07:00,322 DEBUG quick_setup starting in /data/MGL1111/proc/os75bb 2011-09-02 16:07:00,322 DEBUG quick_setup executing commands from /data/MGL1111/proc/os75bb/contour 2011-09-02 16:07:00,322 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_mgl 2011-09-02 16:07:00,869 DEBUG quick_asect done running getmat with "allbins" 2011-09-02 16:07:00,887 INFO root copying NOFIG to /home/adcp/www/figures/os75bb_hcorr_plot.png 2011-09-02 16:07:00,887 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os75bb_hcorr_plot_thumb.png 2011-09-02 16:07:00,887 DEBUG root matfile is contour/contour_uv.mat 2011-09-02 16:07:00,895 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os75bb_cont_uv.mat 2011-09-02 16:07:00,895 DEBUG root matfile is vector/vector_uv.mat 2011-09-02 16:07:00,896 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os75bb_vect_uv.mat 2011-09-02 16:07:00,897 DEBUG root matfile is contour/contour_xy.mat 2011-09-02 16:07:00,897 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os75bb_cont_xy.mat 2011-09-02 16:07:00,897 DEBUG root matfile is vector/vector_xy.mat 2011-09-02 16:07:00,897 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os75bb_vect_xy.mat 2011-09-02 16:07:00,897 DEBUG root about to copy file edit/a_mgl.tem to /home/adcp/www/data/os75bb_temp.asc 2011-09-02 16:07:00,898 INFO root copying edit/a_mgl.tem to /home/adcp/www/data/os75bb_temp.asc 2011-09-02 16:07:01,766 DEBUG root about to copy netcdf file /home/data/MGL1111/proc/os75bb/contour/os75bb.nc to /home/adcp/www/data/os75bb.nc 2011-09-02 16:07:01,789 INFO root copying edit/a_mgl.tem to /home/adcp/www/data/os75bb.nc 2011-09-02 16:07:01,828 INFO root generating pingstats for os75bb 2011-09-02 16:07:01,828 INFO root Ending quick_adcp.py