2012-02-28 19:54:35,435 DEBUG root about to write control file parameters to --yearbase 2012 --cruisename MGL1204 --configtype python --sonar os75bb --dbname a_mgl --datatype uhdas --cfgpath /home/data/MGL1204/proc/os75bb/config --ens_len 300 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea --skip_avg ## see above --max_search_depth 1000 --proc_engine python --incremental --find_pflags --hidedisplay --top_plotbin 1 --auto 2012-02-28 19:54:35,435 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d os75bb 2012-02-28 19:54:35,437 DEBUG quick_adcp progdir = /home/currents/programs 2012-02-28 19:54:35,437 DEBUG quick_adcp binos = lnx64 2012-02-28 19:54:35,438 DEBUG quick_setup found cruise_info.hcorr (seapath, sea, 0) 2012-02-28 19:54:35,440 INFO quick_adcp importing numpy 2012-02-28 19:54:35,457 INFO quick_adcp importing matplotlib 2012-02-28 19:54:35,528 DEBUG quick_mpl in Q_mpl 2012-02-28 19:54:35,528 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 2012-02-28 19:54:35,528 INFO quick_adcp cwd is /data/MGL1204/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 2012-02-28 19:54:35,528 INFO quick_adcp original fix file is a_mgl.gps 2012-02-28 19:54:35,528 INFO quick_adcp smoothed nav file is a_mgl_refsm.asc 2012-02-28 19:54:35,528 DEBUG quick_asect extracting matlab files for os75, bb pings 2012-02-28 19:54:35,547 DEBUG quick_setup data directory: /home/data/MGL1204/raw/os75 2012-02-28 19:54:35,550 INFO quick_setup found 323 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/MGL1204/raw/os75/*.raw" 2012-02-28 19:54:35,552 DEBUG quick_setup found 323 files from original filelist 2012-02-28 19:54:35,552 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/MGL1204/raw/os75/mgl2012_031_85171.raw ... 2012-02-28 19:54:35,554 DEBUG quick_adcp Tue Feb 28 19:54:35 2012 running quick_adcp.py as follows: --cntfile /home/data/MGL1204/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 2012 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/MGL1204/proc/os75bb/config cntfile /home/data/MGL1204/proc/os75bb/os75bb_qpy.cnt commands None configtype python cruisename MGL1204 data_def vmadcp.def datadir /home/data/MGL1204/raw/os75 datafile_glob *.raw datatype uhdas dbname a_mgl 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/MGL1204/raw/os75/mgl2012_031_85171.raw', '/home/data/MGL1204/raw/os75/mgl2012_032_00000.raw', '/home/data/MGL1204/raw/os75/mgl2012_032_07200.raw', '/home/data/MGL1204/raw/os75/mgl2012_032_14400.raw', 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'/home/data/MGL1204/raw/os75/mgl2012_057_64800.raw', '/home/data/MGL1204/raw/os75/mgl2012_057_72000.raw', '/home/data/MGL1204/raw/os75/mgl2012_057_79200.raw', '/home/data/MGL1204/raw/os75/mgl2012_058_00000.raw', '/home/data/MGL1204/raw/os75/mgl2012_058_07200.raw', '/home/data/MGL1204/raw/os75/mgl2012_058_14400.raw', '/home/data/MGL1204/raw/os75/mgl2012_058_21600.raw', '/home/data/MGL1204/raw/os75/mgl2012_058_28800.raw', '/home/data/MGL1204/raw/os75/mgl2012_058_36000.raw', '/home/data/MGL1204/raw/os75/mgl2012_058_43200.raw', '/home/data/MGL1204/raw/os75/mgl2012_058_50400.raw', '/home/data/MGL1204/raw/os75/mgl2012_058_57600.raw', '/home/data/MGL1204/raw/os75/mgl2012_058_64800.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 23 fixfile a_mgl.gps frequency 75 gbin_style python gbindirbase /home/data/MGL1204/gbin hcorr_inst seapath help False hidedisplay True incremental True instname os75 jitter 15 max_BLKprofiles 300 max_search_depth 1000 maxrunsecs None min_filter_fraction 0.5 model os nosave_editcfg 0 num_persistence 24 numbins 128 overview False pgmin 50 ping_headcorr False pingtype bb post_headcorr None printformats png proc_engine python proc_yearbase 2012 progdir /home/currents/programs py_gbindirbase /home/data/MGL1204/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 2012 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 2012-02-28 19:54:35,554 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:35,554 INFO quick_adcp step 1: set up editing files 2012-02-28 19:54:35,554 DEBUG quick_run executing commands from /data/MGL1204/proc/os75bb/edit 2012-02-28 19:54:35,554 DEBUG quick_run setup.m exists. not replacing 2012-02-28 19:54:35,554 DEBUG quick_run asetup.m exists. not replacing 2012-02-28 19:54:35,554 DEBUG quick_run aflagit_setup.m exists. not replacing 2012-02-28 19:54:35,555 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 2012-02-28 19:54:35,555 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:35,555 INFO quick_adcp step 2: scan files for time range 2012-02-28 19:54:35,555 INFO quick_adcp about to run numpy scan, requiring python gbins 2012-02-28 19:54:35,555 DEBUG quick_npy Starting: scanping 2012-02-28 19:54:36,022 DEBUG quick_npy Ending: scanping 2012-02-28 19:54:36,024 DEBUG quick_subs start_end_time 2012/02/01 23:39:35 to 2012/02/01 23:49:46 2012-02-28 19:54:36,024 DEBUG quick_subs dd0: 31.985822 dd1: 31.992894 2012-02-28 19:54:36,024 INFO quick_adcp in quick_adcp.py: after scan; look for database times in /data/MGL1204/proc/os75bb 2012-02-28 19:54:36,024 INFO quick_adcp looking for database with adcpdb/a_mgl*.blk 2012-02-28 19:54:36,025 INFO quick_adcp database found: listing blocks 2012-02-28 19:54:36,025 DEBUG quick_subs removing a_mgldir.blk 2012-02-28 19:54:36,025 DEBUG quick_subs about to run mkblkdir 2012-02-28 19:54:36,025 DEBUG quick_subs database still exists; rerunning mkdirblk 2012-02-28 19:54:36,025 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2012-02-28 19:54:36,038 DEBUG quick_subs database passes. 2012-02-28 19:54:36,038 DEBUG quick_subs start_end_time 2012/02/01 23:44:32 to 2012/02/28 19:34:33 2012-02-28 19:54:36,038 DEBUG quick_subs dd0: 31.989259 dd1: 58.815660 2012-02-28 19:54:36,039 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2012-02-28 19:54:36,039 DEBUG quick_adcp origdb_time_range is 2012/02/01 23:44:32 to 2012/02/28 19:34:33 2012-02-28 19:54:36,039 DEBUG quick_adcp (31.989259 to 58.815660) 2012-02-28 19:54:36,039 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:36,039 INFO quick_adcp step 3: generate averaged data... 2012-02-28 19:54:36,039 DEBUG quick_run file load/ping_editparams.txt exists. not replacing 2012-02-28 19:54:36,040 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:36,040 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/load 2012-02-28 19:54:36,040 DEBUG quick_setup running python command "run_pingavg_npy" 2012-02-28 19:54:36,040 DEBUG quick_npy Starting: pingavg 2012-02-28 19:54:36,042 DEBUG quick_npy singleping editing parameters: 2012-02-28 19:54:36,042 DEBUG quick_npy bigtarget_mab_window : 11 2012-02-28 19:54:36,043 DEBUG quick_npy rl_endbin : 20 2012-02-28 19:54:36,043 DEBUG quick_npy max_search_depth : 1000 2012-02-28 19:54:36,043 DEBUG quick_npy cor_cutoff : 120 2012-02-28 19:54:36,043 DEBUG quick_npy ampfilt : 40 2012-02-28 19:54:36,043 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2012-02-28 19:54:36,043 DEBUG quick_npy rl_startbin : 2 2012-02-28 19:54:36,043 DEBUG quick_npy ecutoff : 1 2012-02-28 19:54:36,043 DEBUG quick_npy refavg_valcutoff : 1 2012-02-28 19:54:36,044 DEBUG quick_npy weakprof_percent : 30 2012-02-28 19:54:36,044 DEBUG quick_npy bigtarget_ampthresh : 55 2012-02-28 19:54:36,051 INFO pingavg Pingavg.run for time range 58.750042 to 58.826297 2012-02-28 19:54:36,080 DEBUG pingavg Chunk 1 of 1, 58.750042 to 58.826297 2012-02-28 19:54:36,080 DEBUG pingavg Nothing written 2012-02-28 19:54:36,080 DEBUG quick_npy wrote 0 averages 2012-02-28 19:54:36,081 DEBUG quick_npy Ending: pingavg 2012-02-28 19:54:36,081 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:36,081 INFO quick_adcp step 4: load averaged data (to database) 2012-02-28 19:54:36,082 DEBUG quick_subs in del_overlapping 2012-02-28 19:54:36,082 DEBUG quick_subs lastblock: 2012-02-28 19:54:36,082 DEBUG quick_subs 26 2012-02-28 19:54:36,082 DEBUG quick_subs lastcmd: 2012-02-28 19:54:36,082 DEBUG quick_subs 26 2012-02-28 19:54:36,082 DEBUG quick_subs delblks: 2012-02-28 19:54:36,082 DEBUG quick_subs [26] 2012-02-28 19:54:36,082 DEBUG quick_subs loadblks: 2012-02-28 19:54:36,082 DEBUG quick_subs [26] 2012-02-28 19:54:36,083 DEBUG quick_subs about to run mkblkdir 2012-02-28 19:54:36,083 DEBUG quick_subs database still exists; rerunning mkdirblk 2012-02-28 19:54:36,084 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2012-02-28 19:54:36,096 DEBUG quick_subs database passes. 2012-02-28 19:54:36,096 DEBUG quick_subs start_end_time 2012/02/01 23:44:32 to 2012/02/28 00:39:33 2012-02-28 19:54:36,096 DEBUG quick_subs dd0: 31.989259 dd1: 58.027465 2012-02-28 19:54:36,097 DEBUG quick_run [26] 2012-02-28 19:54:36,097 DEBUG quick_run cmdlist 2012-02-28 19:54:36,097 DEBUG quick_run ['./ens_blk026.cmd'] 2012-02-28 19:54:36,100 INFO quick_run Warning: 1 files will be loaded; 26 already exist 2012-02-28 19:54:36,100 INFO quick_run Tue Feb 28 19:54:36 2012 2012-02-28 19:54:36,101 INFO quick_run about to load uhdas files 2012-02-28 19:54:36,101 INFO quick_run /home/data/MGL1204/raw/os75/mgl2012_031_85171.raw /home/data/MGL1204/raw/os75/mgl2012_032_00000.raw /home/data/MGL1204/raw/os75/mgl2012_032_07200.raw /home/data/MGL1204/raw/os75/mgl2012_032_14400.raw /home/data/MGL1204/raw/os75/mgl2012_032_21600.raw ... 2012-02-28 19:54:36,101 DEBUG quick_setup load/ldcodas.tmp exists 2012-02-28 19:54:36,101 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:36,101 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/load 2012-02-28 19:54:36,101 DEBUG quick_setup running python command "ldcodas" 2012-02-28 19:54:36,101 DEBUG quick_subs filling "thisload" timerange 2012-02-28 19:54:36,104 DEBUG quick_subs in ldcodas 2012-02-28 19:54:36,104 DEBUG quick_subs cmdlist: 2012-02-28 19:54:36,104 DEBUG quick_subs ['./ens_blk026.cmd'] 2012-02-28 19:54:36,104 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_mgl DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2012 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk026.cmd 2012-02-28 19:54:36,104 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/ldcodas ldcodas.tmp 2012-02-28 19:54:36,146 DEBUG quick_subs removing a_mgldir.blk 2012-02-28 19:54:36,146 DEBUG quick_subs about to run mkblkdir 2012-02-28 19:54:36,147 DEBUG quick_subs database still exists; rerunning mkdirblk 2012-02-28 19:54:36,147 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2012-02-28 19:54:36,159 DEBUG quick_subs database passes. 2012-02-28 19:54:36,160 DEBUG quick_subs start_end_time 2012/02/01 23:44:32 to 2012/02/28 19:49:32 2012-02-28 19:54:36,160 DEBUG quick_subs dd0: 31.989259 dd1: 58.826065 2012-02-28 19:54:36,160 INFO quick_adcp loaded_time_range is 2012/02/01 23:44:32 to 2012/02/28 19:49:32 2012-02-28 19:54:36,160 INFO quick_adcp (31.989259 to 58.826065) 2012-02-28 19:54:36,160 INFO quick_adcp origdb_time_range is 2012/02/01 23:44:32 to 2012/02/28 19:34:33 2012-02-28 19:54:36,160 INFO quick_adcp (31.989259 to 58.815660) 2012-02-28 19:54:36,161 INFO quick_adcp thisload_time_range is 2012/02/28 00:44:31 to 2012/02/28 19:49:32 2012-02-28 19:54:36,161 INFO quick_adcp (58.030914 to 58.030914) 2012-02-28 19:54:36,161 INFO quick_adcp --------------------- 2012-02-28 19:54:36,161 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:36,161 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/adcpdb 2012-02-28 19:54:36,161 DEBUG quick_setup running python command "lst_conf" 2012-02-28 19:54:36,162 DEBUG quick_subs dbname: a_mgl output: a_mgl.cnh time_ranges: all 2012-02-28 19:54:36,162 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_conf lst_conf.tmp 2012-02-28 19:54:39,969 DEBUG quick_setup found (in edit/asetup.m): 2012-02-28 19:54:39,969 DEBUG quick_setup config.beamangle is 30 2012-02-28 19:54:39,969 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:39,970 INFO quick_adcp step 5: set up files for gautoedit.py 2012-02-28 19:54:39,970 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2012-02-28 19:54:39,970 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:39,970 INFO quick_adcp step 6: set up files for gautoedit.py 2012-02-28 19:54:39,970 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:39,970 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/edit 2012-02-28 19:54:39,970 DEBUG quick_setup running python command "setflags" 2012-02-28 19:54:39,970 DEBUG quick_subs dbname: ../adcpdb/a_mgl pg_min: 50 set_range_bit time_ranges: all 2012-02-28 19:54:39,971 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2012-02-28 19:54:40,034 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:40,034 INFO quick_adcp step 7: get navigation 2012-02-28 19:54:40,034 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:40,034 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/nav 2012-02-28 19:54:40,035 DEBUG quick_setup running python command "catnav" 2012-02-28 19:54:40,039 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2012-02-28 19:54:40,039 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:40,039 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/cal/rotate 2012-02-28 19:54:40,040 DEBUG quick_setup running python command "lst_hdg" 2012-02-28 19:54:40,040 DEBUG quick_subs dbname: ../../adcpdb/a_mgl output: scn.hdg step_size= 1 year_base= 2012 time_ranges: all 2012-02-28 19:54:40,040 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_hdg lst_hdg.tmp 2012-02-28 19:54:40,086 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:40,086 INFO quick_adcp step 8: get heading correction 2012-02-28 19:54:40,087 DEBUG quick_run hcorr_inst is seapath 2012-02-28 19:54:40,087 DEBUG quick_mpl Starting plot: hcorr 2012-02-28 19:54:40,180 DEBUG quick_mplplots found 26.836805 days of data 2012-02-28 19:54:40,180 DEBUG quick_mplplots figures with 4 panels per page, 1.000000 days per panel 2012-02-28 19:54:40,180 DEBUG quick_mplplots printing 7 pages 2012-02-28 19:54:40,890 DEBUG quick_mpl Ending plot: hcorr 2012-02-28 19:54:40,891 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:40,891 INFO quick_adcp step 9: rotate velocities 2012-02-28 19:54:40,891 DEBUG quick_setup cal/rotate/norotate.tmp exists 2012-02-28 19:54:40,891 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:40,891 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/cal/rotate 2012-02-28 19:54:40,891 DEBUG quick_setup running python command "norotate" 2012-02-28 19:54:40,891 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: 2012/02/01 23:44:32 to 2012/02/28 19:49:32 OPTION_LIST: water_and_bottom_track: year_base= 2012 /* time_angle_file: time_angle.ang */ amplitude= 1.0 angle_0= 0.0 end end 2012-02-28 19:54:40,892 DEBUG quick_setup about to run echo "writing dummy rotate file" 2012-02-28 19:54:40,896 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:40,896 INFO quick_adcp step 10: nav steps: run adcpsect 2012-02-28 19:54:40,897 DEBUG quick_setup nav/as_nav.tmp exists 2012-02-28 19:54:40,897 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:40,897 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/nav 2012-02-28 19:54:40,897 DEBUG quick_setup running python command "as_nav" 2012-02-28 19:54:40,897 DEBUG quick_subs dbname: ../adcpdb/a_mgl output: a_mgl step_size: 1 ndepth: 20 time_ranges: separate year_base= 2012 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 2012/02/01 23:44:32 to 2012/02/28 19:49:32 /* the whole time range */ 2012-02-28 19:54:40,897 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2012-02-28 19:54:40,980 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:40,981 INFO quick_adcp step 11: nav steps: run refabs 2012-02-28 19:54:40,981 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:40,981 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/nav 2012-02-28 19:54:40,981 DEBUG quick_setup running python command "refabs" 2012-02-28 19:54:40,981 DEBUG quick_subs fix_file_type: simple reference_file: a_mgl.nav fix_file: a_mgl.gps output: a_mgl.ref year_base= 2012 ensemble_length= 300 gap_tolerance= 10 2012-02-28 19:54:40,982 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2012-02-28 19:54:41,057 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:41,057 INFO quick_adcp step 12: nav steps: run smoothr for plots 2012-02-28 19:54:41,058 DEBUG quick_setup nav/smoothr.tmp exists 2012-02-28 19:54:41,058 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:41,058 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/nav 2012-02-28 19:54:41,058 DEBUG quick_setup running python command "smoothr" 2012-02-28 19:54:41,058 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 2012-02-28 19:54:41,058 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2012-02-28 19:54:41,408 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:41,409 INFO quick_adcp step 13: nav steps: smooth navigation 2012-02-28 19:54:41,409 INFO quick_adcp about to run numpy refsm 2012-02-28 19:54:41,409 DEBUG quick_npy Starting: refsm 2012-02-28 19:54:41,671 DEBUG nav dtmin = -0.50 dtmax = 3.54 2012-02-28 19:54:41,973 DEBUG quick_npy Ending: refsm 2012-02-28 19:54:41,973 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:41,973 INFO quick_adcp step 14: nav steps: put smoothed nav into codasdb 2012-02-28 19:54:41,974 DEBUG quick_setup nav/putnav.tmp exists 2012-02-28 19:54:41,974 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:41,974 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/nav 2012-02-28 19:54:41,974 DEBUG quick_setup running python command "putnav" 2012-02-28 19:54:41,974 DEBUG quick_subs dbname: ../adcpdb/a_mgl position_file: a_mgl_refsm.asc year_base= 2012 tolerance= 5 navigation_sources: gps end 2012-02-28 19:54:41,974 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2012-02-28 19:54:42,074 INFO quick_adcp plotting navigation 2012-02-28 19:54:42,074 DEBUG quick_mpl Starting plot: nav 2012-02-28 19:54:42,479 DEBUG quick_mpl Ending plot: nav 2012-02-28 19:54:42,480 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:42,480 INFO quick_adcp step 15: nav steps: make reflayer plots 2012-02-28 19:54:42,480 DEBUG quick_mpl Starting plot: refl 2012-02-28 19:54:42,702 DEBUG quick_mplplots found 26.826355 days of data 2012-02-28 19:54:42,702 DEBUG quick_mplplots start day is 31.000000 2012-02-28 19:54:42,702 DEBUG quick_mplplots figures with 2.000000 days per page 2012-02-28 19:54:42,702 DEBUG quick_mplplots printing 14 pages 2012-02-28 19:54:42,702 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2012-02-28 19:54:43,402 DEBUG quick_mpl Ending plot: refl 2012-02-28 19:54:43,402 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:43,439 INFO quick_adcp step 16: find profile flags 2012-02-28 19:54:43,440 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:43,440 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/edit 2012-02-28 19:54:43,440 DEBUG quick_setup running python command "run_autoedit_npy" 2012-02-28 19:54:43,440 DEBUG quick_npy Starting: autoedit 2012-02-28 19:54:43,723 DEBUG pingedit wrote 2 bad bins to abadbin_tmp.asc 2012-02-28 19:54:43,746 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2012-02-28 19:54:43,746 DEBUG quick_npy Ending: autoedit 2012-02-28 19:54:43,746 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:43,746 INFO quick_adcp step 17: apply editing 2012-02-28 19:54:43,746 DEBUG quick_run starting in: /data/MGL1204/proc/os75bb 2012-02-28 19:54:43,746 DEBUG quick_run executing commands from: edit 2012-02-28 19:54:43,748 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/dbupdate ../adcpdb/a_mgl abadprf_tmp.asc 2012-02-28 19:54:43,754 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/badbin ../adcpdb/a_mgl abadbin_tmp.asc 2012-02-28 19:54:44,443 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/set_lgb ../adcpdb/a_mgl 30 2012-02-28 19:54:44,450 DEBUG quick_subs dbname: ../adcpdb/a_mgl pg_min: 50 set_range_bit time_ranges: all 2012-02-28 19:54:44,450 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2012-02-28 19:54:44,514 DEBUG quick_run changing directories back to /data/MGL1204/proc/os75bb 2012-02-28 19:54:44,514 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:44,514 INFO quick_adcp step 18: run nav steps 2012-02-28 19:54:44,514 DEBUG quick_setup nav/as_nav.tmp exists 2012-02-28 19:54:44,514 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:44,514 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/nav 2012-02-28 19:54:44,515 DEBUG quick_setup running python command "as_nav" 2012-02-28 19:54:44,515 DEBUG quick_subs dbname: ../adcpdb/a_mgl output: a_mgl step_size: 1 ndepth: 20 time_ranges: separate year_base= 2012 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 2012/02/01 23:44:32 to 2012/02/28 19:49:32 /* the whole time range */ 2012-02-28 19:54:44,515 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2012-02-28 19:54:44,598 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:44,598 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/nav 2012-02-28 19:54:44,598 DEBUG quick_setup running python command "refabs" 2012-02-28 19:54:44,598 DEBUG quick_subs fix_file_type: simple reference_file: a_mgl.nav fix_file: a_mgl.gps output: a_mgl.ref year_base= 2012 ensemble_length= 300 gap_tolerance= 10 2012-02-28 19:54:44,598 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2012-02-28 19:54:44,670 DEBUG quick_setup nav/smoothr.tmp exists 2012-02-28 19:54:44,670 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:44,671 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/nav 2012-02-28 19:54:44,671 DEBUG quick_setup running python command "smoothr" 2012-02-28 19:54:44,671 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 2012-02-28 19:54:44,671 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2012-02-28 19:54:45,017 DEBUG quick_npy Starting: refsm 2012-02-28 19:54:45,271 DEBUG nav dtmin = -0.50 dtmax = 3.54 2012-02-28 19:54:45,570 DEBUG quick_npy Ending: refsm 2012-02-28 19:54:45,570 DEBUG quick_setup nav/putnav.tmp exists 2012-02-28 19:54:45,571 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:45,571 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/nav 2012-02-28 19:54:45,571 DEBUG quick_setup running python command "putnav" 2012-02-28 19:54:45,571 DEBUG quick_subs dbname: ../adcpdb/a_mgl position_file: a_mgl_refsm.asc year_base= 2012 tolerance= 5 navigation_sources: gps end 2012-02-28 19:54:45,571 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2012-02-28 19:54:45,672 DEBUG quick_mpl Starting plot: nav 2012-02-28 19:54:46,080 DEBUG quick_mpl Ending plot: nav 2012-02-28 19:54:46,080 DEBUG quick_mpl Starting plot: refl 2012-02-28 19:54:46,303 DEBUG quick_mplplots found 26.826355 days of data 2012-02-28 19:54:46,303 DEBUG quick_mplplots start day is 31.000000 2012-02-28 19:54:46,303 DEBUG quick_mplplots figures with 2.000000 days per page 2012-02-28 19:54:46,303 DEBUG quick_mplplots printing 14 pages 2012-02-28 19:54:46,303 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2012-02-28 19:54:47,003 DEBUG quick_mpl Ending plot: refl 2012-02-28 19:54:47,003 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:47,004 INFO quick_adcp step 19: plot temperature 2012-02-28 19:54:47,004 DEBUG quick_setup edit/lst_temp.tmp exists 2012-02-28 19:54:47,004 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:47,004 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/edit 2012-02-28 19:54:47,004 DEBUG quick_setup running python command "lst_temp" 2012-02-28 19:54:47,004 DEBUG quick_subs dbname: ../adcpdb/a_mgl output: a_mgl.tem step_size= 1 year_base= 2012 time_ranges: all 2012-02-28 19:54:47,005 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_temp lst_temp.tmp 2012-02-28 19:54:47,058 DEBUG quick_mpl Starting plot: temp 2012-02-28 19:54:47,134 DEBUG quick_mplplots plotting 7730 points 2012-02-28 19:54:47,394 DEBUG quick_mpl Ending plot: temp 2012-02-28 19:54:47,394 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:47,395 INFO quick_adcp step 20: run calibration steps 2012-02-28 19:54:47,395 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2012-02-28 19:54:47,395 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:47,395 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/cal/botmtrk 2012-02-28 19:54:47,395 DEBUG quick_setup running python command "lst_btrk" 2012-02-28 19:54:47,395 DEBUG quick_subs dbname: ../../adcpdb/a_mgl output: a_mgl.btm step_size= 1 year_base= 2012 time_ranges: 2012/02/01 23:44:32 to 2012/02/28 19:49:32 /* whole time range */ 2012-02-28 19:54:47,396 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_btrk lst_btrk.tmp 2012-02-28 19:54:47,416 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2012-02-28 19:54:47,417 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:47,417 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/cal/botmtrk 2012-02-28 19:54:47,417 DEBUG quick_setup running python command "refabsbt" 2012-02-28 19:54:47,417 DEBUG quick_subs fix_file_type: simple reference_file: a_mgl.btm fix_file: ../../nav/a_mgl.gps output: a_mgl.ref year_base= 2012 ensemble_length= 300 gap_tolerance= 60 2012-02-28 19:54:47,417 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabsbt refabsbt.tmp 2012-02-28 19:54:47,423 DEBUG quick_mpl Starting plot: btcal 2012-02-28 19:54:47,424 DEBUG quick_mplplots No data in a_mgl.btm 2012-02-28 19:54:47,424 DEBUG quick_mplplots Returning from Btplot with no output 2012-02-28 19:54:47,424 DEBUG quick_mpl Ending plot: btcal 2012-02-28 19:54:47,424 DEBUG quick_setup nav/as_nav.tmp exists 2012-02-28 19:54:47,424 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:47,424 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/nav 2012-02-28 19:54:47,424 DEBUG quick_setup running python command "as_nav" 2012-02-28 19:54:47,424 DEBUG quick_subs dbname: ../adcpdb/a_mgl output: a_mgl step_size: 1 ndepth: 20 time_ranges: separate year_base= 2012 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 2012/02/01 23:44:32 to 2012/02/28 19:49:32 /* the whole time range */ 2012-02-28 19:54:47,425 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2012-02-28 19:54:47,511 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2012-02-28 19:54:47,511 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:47,511 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/cal/watertrk 2012-02-28 19:54:47,512 DEBUG quick_setup running python command "timslip" 2012-02-28 19:54:47,512 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= 2012 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 2012-02-28 19:54:47,512 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timslip timslip.tmp 2012-02-28 19:54:47,544 DEBUG quick_mpl Starting plot: wtcal 2012-02-28 19:54:47,546 DEBUG quick_mplplots Found 32 calibration points 2012-02-28 19:54:48,348 DEBUG quick_mpl Ending plot: wtcal 2012-02-28 19:54:48,348 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:48,348 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/cal/watertrk 2012-02-28 19:54:48,348 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2012-02-28 19:54:48,348 DEBUG quick_npy Starting: guess_xducerxy 2012-02-28 19:54:48,630 DEBUG quick_npy Ending: guess_xducerxy 2012-02-28 19:54:48,631 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:48,633 INFO quick_adcp step 21: extract matlab "allbins" 2012-02-28 19:54:48,633 DEBUG quick_asect ------------ step 18: make matlab files for plotting ------------- 2012-02-28 19:54:48,633 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:48,634 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/vector 2012-02-28 19:54:48,634 DEBUG quick_setup running python command "timegrid" 2012-02-28 19:54:48,634 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_mgl.tmp 2012-02-28 19:54:48,644 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:48,645 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/vector 2012-02-28 19:54:48,645 DEBUG quick_setup running python command "as_vect" 2012-02-28 19:54:48,645 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_vect.tmp 2012-02-28 19:54:48,809 DEBUG quick_asect done making vector matfiles 2012-02-28 19:54:48,810 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:48,810 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/contour 2012-02-28 19:54:48,810 DEBUG quick_setup running python command "timegrid" 2012-02-28 19:54:48,810 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_mgl.tmp 2012-02-28 19:54:48,827 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:48,827 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/contour 2012-02-28 19:54:48,827 DEBUG quick_setup running python command "as_cont" 2012-02-28 19:54:48,827 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_cont.tmp 2012-02-28 19:54:49,078 DEBUG quick_setup starting in /data/MGL1204/proc/os75bb 2012-02-28 19:54:49,078 DEBUG quick_setup executing commands from /data/MGL1204/proc/os75bb/contour 2012-02-28 19:54:49,079 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_mgl 2012-02-28 19:54:49,688 DEBUG quick_asect done running getmat with "allbins" 2012-02-28 19:54:49,689 INFO quick_adcp --------------------------------------------- 2012-02-28 19:54:49,689 INFO quick_adcp step 22: write "cruise_info.txt" 2012-02-28 19:54:49,710 INFO root copying NOFIG to /home/adcp/www/figures/os75bb_hcorr_plot.png 2012-02-28 19:54:49,711 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os75bb_hcorr_plot_thumb.png 2012-02-28 19:54:49,711 DEBUG root matfile is contour/contour_uv.mat 2012-02-28 19:54:49,719 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os75bb_cont_uv.mat 2012-02-28 19:54:49,720 DEBUG root matfile is vector/vector_uv.mat 2012-02-28 19:54:49,721 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os75bb_vect_uv.mat 2012-02-28 19:54:49,721 DEBUG root matfile is contour/contour_xy.mat 2012-02-28 19:54:49,721 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os75bb_cont_xy.mat 2012-02-28 19:54:49,721 DEBUG root matfile is vector/vector_xy.mat 2012-02-28 19:54:49,722 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os75bb_vect_xy.mat 2012-02-28 19:54:49,722 DEBUG root about to copy file edit/a_mgl.tem to /home/adcp/www/data/os75bb_temp.asc 2012-02-28 19:54:49,723 INFO root copying edit/a_mgl.tem to /home/adcp/www/data/os75bb_temp.asc 2012-02-28 19:54:50,729 DEBUG root about to copy netcdf file /home/data/MGL1204/proc/os75bb/contour/os75bb.nc to /home/adcp/www/data/os75bb.nc 2012-02-28 19:54:50,757 INFO root copying edit/a_mgl.tem to /home/adcp/www/data/os75bb.nc 2012-02-28 19:54:50,803 INFO root generating pingstats for os75bb 2012-02-28 19:54:50,803 INFO root Ending quick_adcp.py