2011-12-29 15:24:48,702 DEBUG root about to write control file parameters to --yearbase 2011 --cruisename MGL1115 --configtype python --sonar os75bb --dbname a_mgl --datatype uhdas --cfgpath /home/data/MGL1115/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 2011-12-29 15:24:48,702 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d os75bb 2011-12-29 15:24:48,703 DEBUG quick_adcp progdir = /home/currents/programs 2011-12-29 15:24:48,703 DEBUG quick_adcp binos = lnx64 2011-12-29 15:24:48,705 DEBUG quick_setup found cruise_info.hcorr (seapath, hdg, 0) 2011-12-29 15:24:48,705 INFO quick_adcp importing numpy 2011-12-29 15:24:48,721 INFO quick_adcp importing matplotlib 2011-12-29 15:24:48,895 DEBUG quick_mpl in Q_mpl 2011-12-29 15:24:48,896 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_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 2011-12-29 15:24:48,896 INFO quick_adcp cwd is /data/MGL1115/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 2011-12-29 15:24:48,896 INFO quick_adcp original fix file is a_mgl.gps 2011-12-29 15:24:48,896 INFO quick_adcp smoothed nav file is a_mgl_refsm.asc 2011-12-29 15:24:48,896 DEBUG quick_asect extracting matlab files for os75, bb pings 2011-12-29 15:24:48,919 DEBUG quick_setup data directory: /home/data/MGL1115/raw/os75 2011-12-29 15:24:48,922 INFO quick_setup found 416 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/MGL1115/raw/os75/*.raw" 2011-12-29 15:24:48,924 DEBUG quick_setup found 416 files from original filelist 2011-12-29 15:24:48,924 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/MGL1115/raw/os75/mgl2011_329_68844.raw ... 2011-12-29 15:24:48,926 DEBUG quick_adcp Thu Dec 29 15:24:48 2011 running quick_adcp.py as follows: --cntfile /home/data/MGL1115/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 badbeam 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'/home/data/MGL1115/raw/os75/mgl2011_361_36000.raw', '/home/data/MGL1115/raw/os75/mgl2011_361_43200.raw', '/home/data/MGL1115/raw/os75/mgl2011_361_50400.raw', '/home/data/MGL1115/raw/os75/mgl2011_361_57600.raw', '/home/data/MGL1115/raw/os75/mgl2011_361_64800.raw', '/home/data/MGL1115/raw/os75/mgl2011_361_72000.raw', '/home/data/MGL1115/raw/os75/mgl2011_361_79200.raw', '/home/data/MGL1115/raw/os75/mgl2011_362_00000.raw', '/home/data/MGL1115/raw/os75/mgl2011_362_07200.raw', '/home/data/MGL1115/raw/os75/mgl2011_362_14400.raw', '/home/data/MGL1115/raw/os75/mgl2011_362_21600.raw', '/home/data/MGL1115/raw/os75/mgl2011_362_28800.raw', '/home/data/MGL1115/raw/os75/mgl2011_362_36000.raw', '/home/data/MGL1115/raw/os75/mgl2011_362_43200.raw', '/home/data/MGL1115/raw/os75/mgl2011_362_50400.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 23 fixfile a_mgl.gps frequency 75 gbin_style python gbindirbase /home/data/MGL1115/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/MGL1115/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_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 None xducer_dy None 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 2011-12-29 15:24:48,927 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:48,927 INFO quick_adcp step 1: set up editing files 2011-12-29 15:24:48,927 DEBUG quick_run executing commands from /data/MGL1115/proc/os75bb/edit 2011-12-29 15:24:48,927 DEBUG quick_run setup.m exists. not replacing 2011-12-29 15:24:48,927 DEBUG quick_run asetup.m exists. not replacing 2011-12-29 15:24:48,927 DEBUG quick_run aflagit_setup.m exists. not replacing 2011-12-29 15:24:48,927 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:48,928 INFO quick_adcp step 2: scan files for time range 2011-12-29 15:24:48,928 INFO quick_adcp about to run numpy scan, requiring python gbins 2011-12-29 15:24:48,928 DEBUG quick_npy Starting: scanping 2011-12-29 15:24:49,536 DEBUG quick_npy Ending: scanping 2011-12-29 15:24:49,537 DEBUG quick_subs start_end_time 2011/11/26 19:07:28 to 2011/11/26 19:32:40 2011-12-29 15:24:49,538 DEBUG quick_subs dd0: 329.796852 dd1: 329.814352 2011-12-29 15:24:49,538 INFO quick_adcp in quick_adcp.py: after scan; look for database times in /data/MGL1115/proc/os75bb 2011-12-29 15:24:49,538 INFO quick_adcp looking for database with adcpdb/a_mgl*.blk 2011-12-29 15:24:49,539 INFO quick_adcp database found: listing blocks 2011-12-29 15:24:49,539 DEBUG quick_subs removing a_mgldir.blk 2011-12-29 15:24:49,539 DEBUG quick_subs about to run mkblkdir 2011-12-29 15:24:49,539 DEBUG quick_subs database still exists; rerunning mkdirblk 2011-12-29 15:24:49,540 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2011-12-29 15:24:49,555 DEBUG quick_subs database passes. 2011-12-29 15:24:49,556 DEBUG quick_subs start_end_time 2011/11/26 19:12:27 to 2011/12/29 14:49:50 2011-12-29 15:24:49,556 DEBUG quick_subs dd0: 329.800313 dd1: 362.617940 2011-12-29 15:24:49,557 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2011-12-29 15:24:49,557 DEBUG quick_adcp origdb_time_range is 2011/11/26 19:12:27 to 2011/12/29 14:49:50 2011-12-29 15:24:49,557 DEBUG quick_adcp (329.800313 to 362.617940) 2011-12-29 15:24:49,557 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:49,557 INFO quick_adcp step 3: generate averaged data... 2011-12-29 15:24:49,557 DEBUG quick_run file load/ping_editparams.txt exists. not replacing 2011-12-29 15:24:49,557 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:49,557 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/load 2011-12-29 15:24:49,558 DEBUG quick_setup running python command "run_pingavg_npy" 2011-12-29 15:24:49,558 DEBUG quick_npy Starting: pingavg 2011-12-29 15:24:49,560 DEBUG quick_npy singleping editing parameters: 2011-12-29 15:24:49,560 DEBUG quick_npy bigtarget_mab_window : 11 2011-12-29 15:24:49,560 DEBUG quick_npy rl_endbin : 20 2011-12-29 15:24:49,560 DEBUG quick_npy max_search_depth : 1500 2011-12-29 15:24:49,560 DEBUG quick_npy cor_cutoff : 120 2011-12-29 15:24:49,560 DEBUG quick_npy ampfilt : 40 2011-12-29 15:24:49,560 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2011-12-29 15:24:49,560 DEBUG quick_npy rl_startbin : 2 2011-12-29 15:24:49,560 DEBUG quick_npy ecutoff : 1 2011-12-29 15:24:49,560 DEBUG quick_npy refavg_valcutoff : 1 2011-12-29 15:24:49,560 DEBUG quick_npy weakprof_percent : 30 2011-12-29 15:24:49,561 DEBUG quick_npy bigtarget_ampthresh : 55 2011-12-29 15:24:49,568 INFO pingavg Pingavg.run for time range 362.583342 to 362.638935 2011-12-29 15:24:49,596 DEBUG pingavg Chunk 1 of 1, 362.583342 to 362.638935 2011-12-29 15:24:49,597 DEBUG pingavg Nothing written 2011-12-29 15:24:49,597 DEBUG quick_npy wrote 0 averages 2011-12-29 15:24:49,597 DEBUG quick_npy Ending: pingavg 2011-12-29 15:24:49,598 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:49,598 INFO quick_adcp step 4: load averaged data (to database) 2011-12-29 15:24:49,599 DEBUG quick_subs in del_overlapping 2011-12-29 15:24:49,599 DEBUG quick_subs lastblock: 2011-12-29 15:24:49,599 DEBUG quick_subs 99 2011-12-29 15:24:49,600 DEBUG quick_subs lastcmd: 2011-12-29 15:24:49,600 DEBUG quick_subs 99 2011-12-29 15:24:49,600 DEBUG quick_subs delblks: 2011-12-29 15:24:49,600 DEBUG quick_subs [99] 2011-12-29 15:24:49,600 DEBUG quick_subs loadblks: 2011-12-29 15:24:49,600 DEBUG quick_subs [99] 2011-12-29 15:24:49,601 DEBUG quick_subs about to run mkblkdir 2011-12-29 15:24:49,601 DEBUG quick_subs database still exists; rerunning mkdirblk 2011-12-29 15:24:49,601 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2011-12-29 15:24:49,617 DEBUG quick_subs database passes. 2011-12-29 15:24:49,618 DEBUG quick_subs start_end_time 2011/11/26 19:12:27 to 2011/12/28 21:54:50 2011-12-29 15:24:49,618 DEBUG quick_subs dd0: 329.800313 dd1: 361.913079 2011-12-29 15:24:49,618 DEBUG quick_run [99] 2011-12-29 15:24:49,618 DEBUG quick_run cmdlist 2011-12-29 15:24:49,618 DEBUG quick_run ['./ens_blk099.cmd'] 2011-12-29 15:24:49,621 INFO quick_run Warning: 1 files will be loaded; 99 already exist 2011-12-29 15:24:49,621 INFO quick_run Thu Dec 29 15:24:49 2011 2011-12-29 15:24:49,621 INFO quick_run about to load uhdas files 2011-12-29 15:24:49,621 INFO quick_run /home/data/MGL1115/raw/os75/mgl2011_329_68844.raw /home/data/MGL1115/raw/os75/mgl2011_329_72000.raw /home/data/MGL1115/raw/os75/mgl2011_329_79200.raw /home/data/MGL1115/raw/os75/mgl2011_330_00000.raw /home/data/MGL1115/raw/os75/mgl2011_330_07200.raw ... 2011-12-29 15:24:49,622 DEBUG quick_setup load/ldcodas.tmp exists 2011-12-29 15:24:49,622 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:49,622 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/load 2011-12-29 15:24:49,622 DEBUG quick_setup running python command "ldcodas" 2011-12-29 15:24:49,622 DEBUG quick_subs filling "thisload" timerange 2011-12-29 15:24:49,624 DEBUG quick_subs in ldcodas 2011-12-29 15:24:49,624 DEBUG quick_subs cmdlist: 2011-12-29 15:24:49,624 DEBUG quick_subs ['./ens_blk099.cmd'] 2011-12-29 15:24:49,624 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_blk099.cmd 2011-12-29 15:24:49,624 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/ldcodas ldcodas.tmp 2011-12-29 15:24:49,660 DEBUG quick_subs removing a_mgldir.blk 2011-12-29 15:24:49,660 DEBUG quick_subs about to run mkblkdir 2011-12-29 15:24:49,660 DEBUG quick_subs database still exists; rerunning mkdirblk 2011-12-29 15:24:49,661 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2011-12-29 15:24:49,676 DEBUG quick_subs database passes. 2011-12-29 15:24:49,677 DEBUG quick_subs start_end_time 2011/11/26 19:12:27 to 2011/12/29 15:19:48 2011-12-29 15:24:49,677 DEBUG quick_subs dd0: 329.800313 dd1: 362.638750 2011-12-29 15:24:49,677 INFO quick_adcp loaded_time_range is 2011/11/26 19:12:27 to 2011/12/29 15:19:48 2011-12-29 15:24:49,678 INFO quick_adcp (329.800313 to 362.638750) 2011-12-29 15:24:49,678 INFO quick_adcp origdb_time_range is 2011/11/26 19:12:27 to 2011/12/29 14:49:50 2011-12-29 15:24:49,678 INFO quick_adcp (329.800313 to 362.617940) 2011-12-29 15:24:49,678 INFO quick_adcp thisload_time_range is 2011/12/28 21:59:50 to 2011/12/29 15:19:48 2011-12-29 15:24:49,678 INFO quick_adcp (361.916551 to 361.916551) 2011-12-29 15:24:49,678 INFO quick_adcp --------------------- 2011-12-29 15:24:49,679 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:49,679 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/adcpdb 2011-12-29 15:24:49,679 DEBUG quick_setup running python command "lst_conf" 2011-12-29 15:24:49,679 DEBUG quick_subs dbname: a_mgl output: a_mgl.cnh time_ranges: all 2011-12-29 15:24:49,679 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_conf lst_conf.tmp 2011-12-29 15:24:50,691 DEBUG quick_setup found (in edit/asetup.m): 2011-12-29 15:24:50,691 DEBUG quick_setup config.beamangle is 30 2011-12-29 15:24:50,691 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:50,691 INFO quick_adcp step 5: set up files for gautoedit.py 2011-12-29 15:24:50,691 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2011-12-29 15:24:50,692 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:50,692 INFO quick_adcp step 6: set up files for gautoedit.py 2011-12-29 15:24:50,692 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:50,692 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/edit 2011-12-29 15:24:50,692 DEBUG quick_setup running python command "setflags" 2011-12-29 15:24:50,692 DEBUG quick_subs dbname: ../adcpdb/a_mgl pg_min: 50 set_range_bit time_ranges: all 2011-12-29 15:24:50,692 DEBUG quick_subs dbname: ../adcpdb/a_mgl 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 2011-12-29 15:24:50,693 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2011-12-29 15:24:50,777 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:50,777 INFO quick_adcp step 7: get navigation 2011-12-29 15:24:50,778 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:50,778 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/nav 2011-12-29 15:24:50,778 DEBUG quick_setup running python command "catnav" 2011-12-29 15:24:50,785 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2011-12-29 15:24:50,785 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:50,785 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/cal/rotate 2011-12-29 15:24:50,785 DEBUG quick_setup running python command "lst_hdg" 2011-12-29 15:24:50,785 DEBUG quick_subs dbname: ../../adcpdb/a_mgl output: scn.hdg step_size= 1 year_base= 2011 time_ranges: all 2011-12-29 15:24:50,786 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_hdg lst_hdg.tmp 2011-12-29 15:24:50,836 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:50,837 INFO quick_adcp step 8: get heading correction 2011-12-29 15:24:50,837 DEBUG quick_run hcorr_inst is seapath 2011-12-29 15:24:50,837 DEBUG quick_mpl Starting plot: hcorr 2011-12-29 15:24:50,964 DEBUG quick_mplplots found 32.838438 days of data 2011-12-29 15:24:50,965 DEBUG quick_mplplots figures with 4 panels per page, 1.000000 days per panel 2011-12-29 15:24:50,965 DEBUG quick_mplplots printing 9 pages 2011-12-29 15:24:51,655 DEBUG quick_mpl Ending plot: hcorr 2011-12-29 15:24:51,656 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:51,656 INFO quick_adcp step 9: rotate velocities 2011-12-29 15:24:51,656 DEBUG quick_setup cal/rotate/norotate.tmp exists 2011-12-29 15:24:51,656 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:51,656 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/cal/rotate 2011-12-29 15:24:51,656 DEBUG quick_setup running python command "norotate" 2011-12-29 15:24:51,656 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: 2011/11/26 19:12:27 to 2011/12/29 15:19:48 OPTION_LIST: water_and_bottom_track: year_base= 2011 /* time_angle_file: time_angle.ang */ amplitude= 1.0 angle_0= 0.0 end end 2011-12-29 15:24:51,657 DEBUG quick_setup about to run echo "writing dummy rotate file" 2011-12-29 15:24:51,661 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:51,662 INFO quick_adcp step 10: nav steps: run adcpsect 2011-12-29 15:24:51,662 DEBUG quick_setup nav/as_nav.tmp exists 2011-12-29 15:24:51,662 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:51,662 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/nav 2011-12-29 15:24:51,662 DEBUG quick_setup running python command "as_nav" 2011-12-29 15:24:51,662 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 2011/11/26 19:12:27 to 2011/12/29 15:19:48 /* the whole time range */ 2011-12-29 15:24:51,663 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2011-12-29 15:24:51,846 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:51,979 INFO quick_adcp step 11: nav steps: run refabs 2011-12-29 15:24:51,980 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:51,980 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/nav 2011-12-29 15:24:51,980 DEBUG quick_setup running python command "refabs" 2011-12-29 15:24:51,980 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 2011-12-29 15:24:51,980 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2011-12-29 15:24:52,053 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:52,053 INFO quick_adcp step 12: nav steps: run smoothr for plots 2011-12-29 15:24:52,054 DEBUG quick_setup nav/smoothr.tmp exists 2011-12-29 15:24:52,054 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:52,054 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/nav 2011-12-29 15:24:52,054 DEBUG quick_setup running python command "smoothr" 2011-12-29 15:24:52,054 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 2011-12-29 15:24:52,054 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2011-12-29 15:24:52,417 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:52,418 INFO quick_adcp step 13: nav steps: smooth navigation 2011-12-29 15:24:52,418 INFO quick_adcp about to run numpy refsm 2011-12-29 15:24:52,418 DEBUG quick_npy Starting: refsm 2011-12-29 15:24:52,679 INFO nav dtmin = -0.50 dtmax = 4.46 2011-12-29 15:24:52,989 DEBUG quick_npy Ending: refsm 2011-12-29 15:24:52,989 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:52,990 INFO quick_adcp step 14: nav steps: put smoothed nav into codasdb 2011-12-29 15:24:52,990 DEBUG quick_setup nav/putnav.tmp exists 2011-12-29 15:24:52,990 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:52,990 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/nav 2011-12-29 15:24:52,990 DEBUG quick_setup running python command "putnav" 2011-12-29 15:24:52,990 DEBUG quick_subs dbname: ../adcpdb/a_mgl position_file: a_mgl_refsm.asc year_base= 2011 tolerance= 5 navigation_sources: gps end 2011-12-29 15:24:52,990 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2011-12-29 15:24:53,620 INFO quick_adcp plotting navigation 2011-12-29 15:24:53,620 DEBUG quick_mpl Starting plot: nav 2011-12-29 15:24:54,069 DEBUG quick_mpl Ending plot: nav 2011-12-29 15:24:54,069 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:54,069 INFO quick_adcp step 15: nav steps: make reflayer plots 2011-12-29 15:24:54,069 DEBUG quick_mpl Starting plot: refl 2011-12-29 15:24:54,304 DEBUG quick_mplplots found 32.834969 days of data 2011-12-29 15:24:54,304 DEBUG quick_mplplots start day is 329.000000 2011-12-29 15:24:54,304 DEBUG quick_mplplots figures with 2.000000 days per page 2011-12-29 15:24:54,305 DEBUG quick_mplplots printing 17 pages 2011-12-29 15:24:54,305 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2011-12-29 15:24:54,305 INFO quick_mplplots startdd is 329.0 2011-12-29 15:24:54,305 INFO quick_mplplots dt is 2.0 2011-12-29 15:24:55,032 DEBUG quick_mpl Ending plot: refl 2011-12-29 15:24:55,033 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:55,033 INFO quick_adcp step 16: find profile flags 2011-12-29 15:24:55,033 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:55,033 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/edit 2011-12-29 15:24:55,033 DEBUG quick_setup running python command "run_autoedit_npy" 2011-12-29 15:24:55,034 DEBUG quick_npy Starting: autoedit 2011-12-29 15:24:55,331 DEBUG pingedit wrote 3 bad bins to abadbin_tmp.asc 2011-12-29 15:24:55,355 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2011-12-29 15:24:55,355 DEBUG quick_npy Ending: autoedit 2011-12-29 15:24:55,355 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:55,355 INFO quick_adcp step 17: apply editing 2011-12-29 15:24:55,355 DEBUG quick_run starting in: /data/MGL1115/proc/os75bb 2011-12-29 15:24:55,355 DEBUG quick_run executing commands from: edit 2011-12-29 15:24:55,357 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/dbupdate ../adcpdb/a_mgl abadprf_tmp.asc 2011-12-29 15:24:55,362 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/badbin ../adcpdb/a_mgl abadbin_tmp.asc 2011-12-29 15:24:55,372 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/set_lgb ../adcpdb/a_mgl 30 2011-12-29 15:24:55,380 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2011-12-29 15:24:55,460 DEBUG quick_run changing directories back to /data/MGL1115/proc/os75bb 2011-12-29 15:24:55,460 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:55,460 INFO quick_adcp step 18: run nav steps 2011-12-29 15:24:55,460 DEBUG quick_setup nav/as_nav.tmp exists 2011-12-29 15:24:55,460 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:55,460 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/nav 2011-12-29 15:24:55,461 DEBUG quick_setup running python command "as_nav" 2011-12-29 15:24:55,461 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 2011/11/26 19:12:27 to 2011/12/29 15:19:48 /* the whole time range */ 2011-12-29 15:24:55,461 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2011-12-29 15:24:55,546 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:55,547 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/nav 2011-12-29 15:24:55,547 DEBUG quick_setup running python command "refabs" 2011-12-29 15:24:55,547 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 2011-12-29 15:24:55,547 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2011-12-29 15:24:55,616 DEBUG quick_setup nav/smoothr.tmp exists 2011-12-29 15:24:55,616 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:55,617 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/nav 2011-12-29 15:24:55,617 DEBUG quick_setup running python command "smoothr" 2011-12-29 15:24:55,617 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 2011-12-29 15:24:55,617 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2011-12-29 15:24:55,967 INFO quick_adcp running refsm, for reflayer plots 2011-12-29 15:24:55,967 DEBUG quick_npy Starting: refsm 2011-12-29 15:24:56,214 INFO nav dtmin = -0.50 dtmax = 4.46 2011-12-29 15:24:56,515 DEBUG quick_npy Ending: refsm 2011-12-29 15:24:56,515 DEBUG quick_setup nav/putnav.tmp exists 2011-12-29 15:24:56,515 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:56,515 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/nav 2011-12-29 15:24:56,515 DEBUG quick_setup running python command "putnav" 2011-12-29 15:24:56,515 DEBUG quick_subs dbname: ../adcpdb/a_mgl position_file: a_mgl_refsm.asc year_base= 2011 tolerance= 5 navigation_sources: gps end 2011-12-29 15:24:56,515 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2011-12-29 15:24:56,622 DEBUG quick_mpl Starting plot: nav 2011-12-29 15:24:57,053 DEBUG quick_mpl Ending plot: nav 2011-12-29 15:24:57,054 DEBUG quick_mpl Starting plot: refl 2011-12-29 15:24:57,278 DEBUG quick_mplplots found 32.834969 days of data 2011-12-29 15:24:57,278 DEBUG quick_mplplots start day is 329.000000 2011-12-29 15:24:57,278 DEBUG quick_mplplots figures with 2.000000 days per page 2011-12-29 15:24:57,278 DEBUG quick_mplplots printing 17 pages 2011-12-29 15:24:57,278 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2011-12-29 15:24:57,279 INFO quick_mplplots startdd is 329.0 2011-12-29 15:24:57,279 INFO quick_mplplots dt is 2.0 2011-12-29 15:24:58,504 DEBUG quick_mpl Ending plot: refl 2011-12-29 15:24:58,504 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:58,671 INFO quick_adcp step 19: plot temperature 2011-12-29 15:24:58,672 DEBUG quick_setup edit/lst_temp.tmp exists 2011-12-29 15:24:58,672 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:58,672 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/edit 2011-12-29 15:24:58,672 DEBUG quick_setup running python command "lst_temp" 2011-12-29 15:24:58,672 DEBUG quick_subs dbname: ../adcpdb/a_mgl output: a_mgl.tem step_size= 1 year_base= 2011 time_ranges: all 2011-12-29 15:24:58,672 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_temp lst_temp.tmp 2011-12-29 15:24:58,732 DEBUG quick_mpl Starting plot: temp 2011-12-29 15:24:58,808 DEBUG quick_mplplots plotting 7986 points 2011-12-29 15:24:59,094 DEBUG quick_mpl Ending plot: temp 2011-12-29 15:24:59,094 INFO quick_adcp --------------------------------------------- 2011-12-29 15:24:59,095 INFO quick_adcp step 20: run calibration steps 2011-12-29 15:24:59,095 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2011-12-29 15:24:59,095 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:59,095 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/cal/botmtrk 2011-12-29 15:24:59,095 DEBUG quick_setup running python command "lst_btrk" 2011-12-29 15:24:59,095 DEBUG quick_subs dbname: ../../adcpdb/a_mgl output: a_mgl.btm step_size= 1 year_base= 2011 time_ranges: 2011/11/26 19:12:27 to 2011/12/29 15:19:48 /* whole time range */ 2011-12-29 15:24:59,095 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_btrk lst_btrk.tmp 2011-12-29 15:24:59,117 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2011-12-29 15:24:59,117 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:59,117 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/cal/botmtrk 2011-12-29 15:24:59,117 DEBUG quick_setup running python command "refabsbt" 2011-12-29 15:24:59,117 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 2011-12-29 15:24:59,117 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabsbt refabsbt.tmp 2011-12-29 15:24:59,123 DEBUG quick_mpl Starting plot: btcal 2011-12-29 15:24:59,124 DEBUG quick_mplplots No data in a_mgl.btm 2011-12-29 15:24:59,124 DEBUG quick_mplplots Returning from Btplot with no output 2011-12-29 15:24:59,124 DEBUG quick_mpl Ending plot: btcal 2011-12-29 15:24:59,124 DEBUG quick_setup nav/as_nav.tmp exists 2011-12-29 15:24:59,124 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:59,125 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/nav 2011-12-29 15:24:59,125 DEBUG quick_setup running python command "as_nav" 2011-12-29 15:24:59,125 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 2011/11/26 19:12:27 to 2011/12/29 15:19:48 /* the whole time range */ 2011-12-29 15:24:59,125 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2011-12-29 15:24:59,212 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2011-12-29 15:24:59,212 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:24:59,212 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/cal/watertrk 2011-12-29 15:24:59,212 DEBUG quick_setup running python command "timslip" 2011-12-29 15:24:59,212 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 2011-12-29 15:24:59,212 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timslip timslip.tmp 2011-12-29 15:24:59,244 DEBUG quick_mpl Starting plot: wtcal 2011-12-29 15:24:59,247 DEBUG quick_mplplots Found 87 calibration points 2011-12-29 15:25:00,070 DEBUG quick_mpl Ending plot: wtcal 2011-12-29 15:25:00,070 INFO quick_adcp --------------------------------------------- 2011-12-29 15:25:00,070 INFO quick_adcp step 21: adjust GPS position 2011-12-29 15:25:00,071 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:25:00,071 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/cal/watertrk 2011-12-29 15:25:00,071 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2011-12-29 15:25:00,071 DEBUG quick_npy Starting: guess_xducerxy 2011-12-29 15:25:00,359 DEBUG quick_npy Ending: guess_xducerxy 2011-12-29 15:25:00,359 INFO quick_adcp --------------------------------------------- 2011-12-29 15:25:00,359 INFO quick_adcp step 22: extract matlab "allbins" 2011-12-29 15:25:00,359 DEBUG quick_asect ------------ step 18: make matlab files for plotting ------------- 2011-12-29 15:25:00,359 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:25:00,359 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/vector 2011-12-29 15:25:00,360 DEBUG quick_setup running python command "timegrid" 2011-12-29 15:25:00,360 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_mgl.tmp 2011-12-29 15:25:00,370 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:25:00,370 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/vector 2011-12-29 15:25:00,370 DEBUG quick_setup running python command "as_vect" 2011-12-29 15:25:00,370 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_vect.tmp 2011-12-29 15:25:00,535 DEBUG quick_asect done making vector matfiles 2011-12-29 15:25:00,536 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:25:00,536 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/contour 2011-12-29 15:25:00,536 DEBUG quick_setup running python command "timegrid" 2011-12-29 15:25:00,536 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_mgl.tmp 2011-12-29 15:25:00,551 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:25:00,551 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/contour 2011-12-29 15:25:00,551 DEBUG quick_setup running python command "as_cont" 2011-12-29 15:25:00,551 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_cont.tmp 2011-12-29 15:25:00,801 DEBUG quick_setup starting in /data/MGL1115/proc/os75bb 2011-12-29 15:25:00,802 DEBUG quick_setup executing commands from /data/MGL1115/proc/os75bb/contour 2011-12-29 15:25:00,802 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_mgl 2011-12-29 15:25:01,425 DEBUG quick_asect done running getmat with "allbins" 2011-12-29 15:25:01,425 INFO quick_adcp --------------------------------------------- 2011-12-29 15:25:01,426 INFO quick_adcp step 23: write "cruise_info.txt" 2011-12-29 15:25:01,447 INFO root copying NOFIG to /home/adcp/www/figures/os75bb_hcorr_plot.png 2011-12-29 15:25:01,447 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os75bb_hcorr_plot_thumb.png 2011-12-29 15:25:01,448 DEBUG root matfile is contour/contour_uv.mat 2011-12-29 15:25:01,458 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os75bb_cont_uv.mat 2011-12-29 15:25:01,458 DEBUG root matfile is vector/vector_uv.mat 2011-12-29 15:25:01,459 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os75bb_vect_uv.mat 2011-12-29 15:25:01,460 DEBUG root matfile is contour/contour_xy.mat 2011-12-29 15:25:01,460 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os75bb_cont_xy.mat 2011-12-29 15:25:01,460 DEBUG root matfile is vector/vector_xy.mat 2011-12-29 15:25:01,460 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os75bb_vect_xy.mat 2011-12-29 15:25:01,461 DEBUG root about to copy file edit/a_mgl.tem to /home/adcp/www/data/os75bb_temp.asc 2011-12-29 15:25:01,462 INFO root copying edit/a_mgl.tem to /home/adcp/www/data/os75bb_temp.asc 2011-12-29 15:25:08,323 DEBUG root about to copy netcdf file /home/data/MGL1115/proc/os75bb/contour/os75bb.nc to /home/adcp/www/data/os75bb.nc 2011-12-29 15:25:08,351 INFO root copying edit/a_mgl.tem to /home/adcp/www/data/os75bb.nc 2011-12-29 15:25:08,400 INFO root generating pingstats for os75bb 2011-12-29 15:25:08,400 INFO root Ending quick_adcp.py