2012-05-15 11:21:55,874 DEBUG root about to write control file parameters to --yearbase 2012 --cruisename at20 --configtype python --sonar wh300 --dbname a_at --datatype uhdas --cfgpath /home/data/at20/proc/wh300/config --ens_len 120 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea --skip_avg ## see above --max_search_depth 500 --proc_engine python --incremental --find_pflags --hidedisplay --top_plotbin 1 --auto 2012-05-15 11:21:55,875 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d wh300 2012-05-15 11:21:55,878 DEBUG quick_adcp progdir = /home/currents/programs 2012-05-15 11:21:55,878 DEBUG quick_adcp binos = lnx 2012-05-15 11:21:55,893 DEBUG quick_setup found cruise_info.hcorr (phins, hdg, 0) 2012-05-15 11:21:55,913 INFO quick_adcp importing numpy 2012-05-15 11:21:55,949 INFO quick_adcp importing matplotlib 2012-05-15 11:21:56,132 DEBUG quick_mpl in Q_mpl 2012-05-15 11:21:56,132 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 2012-05-15 11:21:56,133 INFO quick_adcp cwd is /home/data/at20/proc/wh300 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 2012-05-15 11:21:56,133 INFO quick_adcp original fix file is a_at.gps 2012-05-15 11:21:56,133 INFO quick_adcp smoothed nav file is a_at_refsm.asc 2012-05-15 11:21:56,134 DEBUG quick_asect extracting matlab files for wh300, bb pings 2012-05-15 11:21:58,325 DEBUG quick_setup data directory: /home/data/at20/raw/wh300 2012-05-15 11:21:58,352 INFO quick_setup found 628 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/at20/raw/wh300/*.raw" 2012-05-15 11:21:58,428 DEBUG quick_setup found 628 files from original filelist 2012-05-15 11:21:58,433 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/at20/raw/wh300/at2012_083_48871.raw ... 2012-05-15 11:21:58,450 DEBUG quick_adcp Tue May 15 11:21:58 2012 running quick_adcp.py as follows: --cntfile /home/data/at20/proc/wh300/wh300_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_at dbpath ../adcpdb deeper_boundaries [40, 60, 80, 100, 120] firstdepth 11 gridnum 80 increment 2 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 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 20 best_loggerdday_name unix_dday best_utcdday_name dday bindir /home/currents/programs/codas3/bin/lnx binos lnx btrk_step 1 cfgpath /home/data/at20/proc/wh300/config cntfile /home/data/at20/proc/wh300/wh300_qpy.cnt commands None configtype python cruisename at20 data_def vmadcp.def datadir /home/data/at20/raw/wh300 datafile_glob *.raw datatype uhdas dbname a_at 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/at20/raw/wh300/at2012_083_48871.raw', '/home/data/at20/raw/wh300/at2012_083_50400.raw', '/home/data/at20/raw/wh300/at2012_083_57600.raw', '/home/data/at20/raw/wh300/at2012_083_64800.raw', '/home/data/at20/raw/wh300/at2012_083_72000.raw', '/home/data/at20/raw/wh300/at2012_083_79200.raw', '/home/data/at20/raw/wh300/at2012_084_00000.raw', '/home/data/at20/raw/wh300/at2012_084_07200.raw', 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filter_hwidth 0.0208 find_pflags True firstdepth 11 fixfile a_at.gps frequency 300 gbin_style python gbindirbase /home/data/at20/gbin hcorr_inst phins help False hidedisplay True incremental True instname wh300 jitter 15 max_BLKprofiles 300 max_search_depth 500 maxrunsecs None min_filter_fraction 0.5 model wh 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/at20/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_at_refsm.asc sonar wh300 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 2012-05-15 11:21:58,451 INFO quick_adcp --------------------------------------------- 2012-05-15 11:21:58,451 INFO quick_adcp step 1: set up editing files 2012-05-15 11:21:58,452 DEBUG quick_run executing commands from /home/data/at20/proc/wh300/edit 2012-05-15 11:21:58,452 DEBUG quick_run setup.m exists. not replacing 2012-05-15 11:21:58,452 DEBUG quick_run asetup.m exists. not replacing 2012-05-15 11:21:58,452 DEBUG quick_run aflagit_setup.m exists. not replacing 2012-05-15 11:21:58,456 DEBUG quick_subs dbname: ../adcpdb/a_at 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 2012-05-15 11:21:58,457 INFO quick_adcp --------------------------------------------- 2012-05-15 11:21:58,457 INFO quick_adcp step 2: scan files for time range 2012-05-15 11:21:58,458 INFO quick_adcp about to run numpy scan, requiring python gbins 2012-05-15 11:21:58,458 DEBUG quick_npy Starting: scanping 2012-05-15 11:22:16,590 DEBUG quick_npy Ending: scanping 2012-05-15 11:22:16,593 DEBUG quick_subs start_end_time 2012/03/24 13:34:33 to 2012/03/24 13:48:45 2012-05-15 11:22:16,593 DEBUG quick_subs dd0: 83.565660 dd1: 83.575521 2012-05-15 11:22:16,593 INFO quick_adcp in quick_adcp.py: after scan; look for database times in /home/data/at20/proc/wh300 2012-05-15 11:22:16,594 INFO quick_adcp looking for database with adcpdb/a_at*.blk 2012-05-15 11:22:16,596 INFO quick_adcp database found: listing blocks 2012-05-15 11:22:16,596 DEBUG quick_subs removing a_atdir.blk 2012-05-15 11:22:16,597 DEBUG quick_subs about to run mkblkdir 2012-05-15 11:22:16,598 DEBUG quick_subs database still exists; rerunning mkdirblk 2012-05-15 11:22:16,598 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2012-05-15 11:22:16,649 DEBUG quick_subs database passes. 2012-05-15 11:22:16,652 DEBUG quick_subs start_end_time 2012/03/24 13:36:32 to 2012/05/15 09:10:35 2012-05-15 11:22:16,652 DEBUG quick_subs dd0: 83.567037 dd1: 135.382350 2012-05-15 11:22:16,653 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2012-05-15 11:22:16,653 DEBUG quick_adcp origdb_time_range is 2012/03/24 13:36:32 to 2012/05/15 09:10:35 2012-05-15 11:22:16,653 DEBUG quick_adcp (83.567037 to 135.382350) 2012-05-15 11:22:16,653 INFO quick_adcp --------------------------------------------- 2012-05-15 11:22:16,654 INFO quick_adcp step 3: generate averaged data... 2012-05-15 11:22:16,654 DEBUG quick_run file load/ping_editparams.txt exists. not replacing 2012-05-15 11:22:16,654 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:22:16,654 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/load 2012-05-15 11:22:16,655 DEBUG quick_setup running python command "run_pingavg_npy" 2012-05-15 11:22:16,655 DEBUG quick_npy Starting: pingavg 2012-05-15 11:22:16,681 DEBUG quick_npy singleping editing parameters: 2012-05-15 11:22:16,681 DEBUG quick_npy bigtarget_mab_window : 11 2012-05-15 11:22:16,681 DEBUG quick_npy rl_endbin : 20 2012-05-15 11:22:16,682 DEBUG quick_npy max_search_depth : 500 2012-05-15 11:22:16,682 DEBUG quick_npy cor_cutoff : 70 2012-05-15 11:22:16,682 DEBUG quick_npy ampfilt : 40 2012-05-15 11:22:16,682 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2012-05-15 11:22:16,682 DEBUG quick_npy rl_startbin : 2 2012-05-15 11:22:16,682 DEBUG quick_npy ecutoff : 1 2012-05-15 11:22:16,683 DEBUG quick_npy refavg_valcutoff : 1 2012-05-15 11:22:16,683 DEBUG quick_npy weakprof_percent : 30 2012-05-15 11:22:16,683 DEBUG quick_npy bigtarget_ampthresh : 55 2012-05-15 11:22:16,705 INFO pingavg Pingavg.run for time range 135.333331 to 135.383364 2012-05-15 11:22:16,832 DEBUG pingavg Chunk 1 of 1, 135.333331 to 135.383364 2012-05-15 11:22:16,840 DEBUG pingavg Nothing written 2012-05-15 11:22:16,840 DEBUG quick_npy wrote 0 averages 2012-05-15 11:22:16,852 DEBUG quick_npy Ending: pingavg 2012-05-15 11:22:16,853 INFO quick_adcp --------------------------------------------- 2012-05-15 11:22:16,853 INFO quick_adcp step 4: load averaged data (to database) 2012-05-15 11:22:16,861 DEBUG quick_subs in del_overlapping 2012-05-15 11:22:16,861 DEBUG quick_subs lastblock: 2012-05-15 11:22:16,862 DEBUG quick_subs 125 2012-05-15 11:22:16,862 DEBUG quick_subs lastcmd: 2012-05-15 11:22:16,862 DEBUG quick_subs 125 2012-05-15 11:22:16,862 DEBUG quick_subs delblks: 2012-05-15 11:22:16,862 DEBUG quick_subs [125] 2012-05-15 11:22:16,862 DEBUG quick_subs loadblks: 2012-05-15 11:22:16,863 DEBUG quick_subs [125] 2012-05-15 11:22:16,869 DEBUG quick_subs about to run mkblkdir 2012-05-15 11:22:16,869 DEBUG quick_subs database still exists; rerunning mkdirblk 2012-05-15 11:22:16,870 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2012-05-15 11:22:16,930 DEBUG quick_subs database passes. 2012-05-15 11:22:16,935 DEBUG quick_subs start_end_time 2012/03/24 13:36:32 to 2012/05/15 05:34:35 2012-05-15 11:22:16,935 DEBUG quick_subs dd0: 83.567037 dd1: 135.232350 2012-05-15 11:22:16,936 DEBUG quick_run [125] 2012-05-15 11:22:16,936 DEBUG quick_run cmdlist 2012-05-15 11:22:16,937 DEBUG quick_run ['./ens_blk125.cmd'] 2012-05-15 11:22:16,991 INFO quick_run Warning: 1 files will be loaded; 125 already exist 2012-05-15 11:22:16,992 INFO quick_run Tue May 15 11:22:16 2012 2012-05-15 11:22:16,992 INFO quick_run about to load uhdas files 2012-05-15 11:22:16,992 INFO quick_run /home/data/at20/raw/wh300/at2012_083_48871.raw /home/data/at20/raw/wh300/at2012_083_50400.raw /home/data/at20/raw/wh300/at2012_083_57600.raw /home/data/at20/raw/wh300/at2012_083_64800.raw /home/data/at20/raw/wh300/at2012_083_72000.raw ... 2012-05-15 11:22:16,992 DEBUG quick_setup load/ldcodas.tmp exists 2012-05-15 11:22:16,993 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:22:16,993 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/load 2012-05-15 11:22:16,993 DEBUG quick_setup running python command "ldcodas" 2012-05-15 11:22:16,993 DEBUG quick_subs filling "thisload" timerange 2012-05-15 11:22:16,996 DEBUG quick_subs in ldcodas 2012-05-15 11:22:16,996 DEBUG quick_subs cmdlist: 2012-05-15 11:22:16,996 DEBUG quick_subs ['./ens_blk125.cmd'] 2012-05-15 11:22:16,996 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_at DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2012 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk125.cmd 2012-05-15 11:22:16,997 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/ldcodas ldcodas.tmp 2012-05-15 11:22:17,069 DEBUG quick_subs removing a_atdir.blk 2012-05-15 11:22:17,071 DEBUG quick_subs about to run mkblkdir 2012-05-15 11:22:17,071 DEBUG quick_subs database still exists; rerunning mkdirblk 2012-05-15 11:22:17,071 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2012-05-15 11:22:17,101 DEBUG quick_subs database passes. 2012-05-15 11:22:17,104 DEBUG quick_subs start_end_time 2012/03/24 13:36:32 to 2012/05/15 09:10:35 2012-05-15 11:22:17,104 DEBUG quick_subs dd0: 83.567037 dd1: 135.382350 2012-05-15 11:22:17,112 INFO quick_adcp loaded_time_range is 2012/03/24 13:36:32 to 2012/05/15 09:10:35 2012-05-15 11:22:17,112 INFO quick_adcp (83.567037 to 135.382350) 2012-05-15 11:22:17,112 INFO quick_adcp origdb_time_range is 2012/03/24 13:36:32 to 2012/05/15 09:10:35 2012-05-15 11:22:17,113 INFO quick_adcp (83.567037 to 135.382350) 2012-05-15 11:22:17,113 INFO quick_adcp thisload_time_range is 2012/05/15 05:36:35 to 2012/05/15 09:10:35 2012-05-15 11:22:17,113 INFO quick_adcp (135.233738 to 135.233738) 2012-05-15 11:22:17,114 INFO quick_adcp --------------------- 2012-05-15 11:22:17,114 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:22:17,114 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/adcpdb 2012-05-15 11:22:17,114 DEBUG quick_setup running python command "lst_conf" 2012-05-15 11:22:17,115 DEBUG quick_subs dbname: a_at output: a_at.cnh time_ranges: all 2012-05-15 11:22:17,115 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_conf lst_conf.tmp 2012-05-15 11:22:46,489 DEBUG quick_setup found (in edit/asetup.m): 2012-05-15 11:22:46,490 DEBUG quick_setup config.beamangle is 20 2012-05-15 11:22:46,490 INFO quick_adcp --------------------------------------------- 2012-05-15 11:22:46,490 INFO quick_adcp step 5: set up files for gautoedit.py 2012-05-15 11:22:46,491 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2012-05-15 11:22:46,491 INFO quick_adcp --------------------------------------------- 2012-05-15 11:22:46,491 INFO quick_adcp step 6: set up files for gautoedit.py 2012-05-15 11:22:46,491 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:22:46,492 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/edit 2012-05-15 11:22:46,492 DEBUG quick_setup running python command "setflags" 2012-05-15 11:22:46,492 DEBUG quick_subs dbname: ../adcpdb/a_at pg_min: 50 set_range_bit time_ranges: all 2012-05-15 11:22:46,493 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/setflags setflags.tmp 2012-05-15 11:22:47,199 INFO quick_adcp --------------------------------------------- 2012-05-15 11:22:47,199 INFO quick_adcp step 7: get navigation 2012-05-15 11:22:47,200 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:22:47,200 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/nav 2012-05-15 11:22:47,200 DEBUG quick_setup running python command "catnav" 2012-05-15 11:22:49,515 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2012-05-15 11:22:49,516 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:22:49,516 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/cal/rotate 2012-05-15 11:22:49,516 DEBUG quick_setup running python command "lst_hdg" 2012-05-15 11:22:49,517 DEBUG quick_subs dbname: ../../adcpdb/a_at output: scn.hdg step_size= 1 year_base= 2012 time_ranges: all 2012-05-15 11:22:49,517 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_hdg lst_hdg.tmp 2012-05-15 11:22:50,545 INFO quick_adcp --------------------------------------------- 2012-05-15 11:22:50,546 INFO quick_adcp step 8: get heading correction 2012-05-15 11:22:50,546 DEBUG quick_run hcorr_inst is phins 2012-05-15 11:22:50,546 DEBUG quick_mpl Starting plot: hcorr 2012-05-15 11:22:54,066 DEBUG quick_mplplots found 51.815310 days of data 2012-05-15 11:22:54,067 DEBUG quick_mplplots figures with 4 panels per page, 1.000000 days per panel 2012-05-15 11:22:54,067 DEBUG quick_mplplots printing 14 pages 2012-05-15 11:22:57,035 DEBUG quick_mpl Ending plot: hcorr 2012-05-15 11:22:57,036 INFO quick_adcp --------------------------------------------- 2012-05-15 11:22:57,036 INFO quick_adcp step 9: rotate velocities 2012-05-15 11:22:57,037 DEBUG quick_setup cal/rotate/norotate.tmp exists 2012-05-15 11:22:57,037 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:22:57,037 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/cal/rotate 2012-05-15 11:22:57,037 DEBUG quick_setup running python command "norotate" 2012-05-15 11:22:57,038 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_at LOG_FILE: rotate.log TIME_RANGE: 2012/03/24 13:36:32 to 2012/05/15 09:10:35 OPTION_LIST: water_and_bottom_track: year_base= 2012 /* time_angle_file: time_angle.ang */ amplitude= 1.0 angle_0= 0.0 end end 2012-05-15 11:22:57,039 DEBUG quick_setup about to run echo "writing dummy rotate file" 2012-05-15 11:22:57,046 INFO quick_adcp --------------------------------------------- 2012-05-15 11:22:57,046 INFO quick_adcp step 10: nav steps: run adcpsect 2012-05-15 11:22:57,047 DEBUG quick_setup nav/as_nav.tmp exists 2012-05-15 11:22:57,047 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:22:57,047 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/nav 2012-05-15 11:22:57,048 DEBUG quick_setup running python command "as_nav" 2012-05-15 11:22:57,048 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at 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 2012/03/24 13:36:32 to 2012/05/15 09:10:35 /* the whole time range */ 2012-05-15 11:22:57,052 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2012-05-15 11:22:58,310 INFO quick_adcp --------------------------------------------- 2012-05-15 11:22:58,311 INFO quick_adcp step 11: nav steps: run refabs 2012-05-15 11:22:58,311 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:22:58,311 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/nav 2012-05-15 11:22:58,312 DEBUG quick_setup running python command "refabs" 2012-05-15 11:22:58,312 DEBUG quick_subs fix_file_type: simple reference_file: a_at.nav fix_file: a_at.gps output: a_at.ref year_base= 2012 ensemble_length= 300 gap_tolerance= 10 2012-05-15 11:22:58,313 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabs refabs.tmp 2012-05-15 11:22:59,264 INFO quick_adcp --------------------------------------------- 2012-05-15 11:22:59,265 INFO quick_adcp step 12: nav steps: run smoothr for plots 2012-05-15 11:22:59,265 DEBUG quick_setup nav/smoothr.tmp exists 2012-05-15 11:22:59,266 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:22:59,266 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/nav 2012-05-15 11:22:59,266 DEBUG quick_setup running python command "smoothr" 2012-05-15 11:22:59,266 DEBUG quick_subs reference_file: a_at.nav refabs_output: a_at.ref output: a_at.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 2012-05-15 11:22:59,267 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/smoothr smoothr.tmp 2012-05-15 11:23:05,918 INFO quick_adcp --------------------------------------------- 2012-05-15 11:23:05,918 INFO quick_adcp step 13: nav steps: smooth navigation 2012-05-15 11:23:05,919 INFO quick_adcp about to run numpy refsm 2012-05-15 11:23:05,919 DEBUG quick_npy Starting: refsm 2012-05-15 11:23:09,519 DEBUG nav dtmin = -0.50 dtmax = 0.55 2012-05-15 11:23:15,943 DEBUG quick_npy Ending: refsm 2012-05-15 11:23:15,944 INFO quick_adcp --------------------------------------------- 2012-05-15 11:23:15,944 INFO quick_adcp step 14: nav steps: put smoothed nav into codasdb 2012-05-15 11:23:15,944 DEBUG quick_setup nav/putnav.tmp exists 2012-05-15 11:23:15,946 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:23:15,946 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/nav 2012-05-15 11:23:15,947 DEBUG quick_setup running python command "putnav" 2012-05-15 11:23:15,947 DEBUG quick_subs dbname: ../adcpdb/a_at position_file: a_at_refsm.asc year_base= 2012 tolerance= 5 navigation_sources: gps end 2012-05-15 11:23:15,947 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/putnav putnav.tmp 2012-05-15 11:23:17,543 INFO quick_adcp plotting navigation 2012-05-15 11:23:17,543 DEBUG quick_mpl Starting plot: nav 2012-05-15 11:23:20,735 DEBUG quick_mpl Ending plot: nav 2012-05-15 11:23:20,735 INFO quick_adcp --------------------------------------------- 2012-05-15 11:23:20,736 INFO quick_adcp step 15: nav steps: make reflayer plots 2012-05-15 11:23:20,736 DEBUG quick_mpl Starting plot: refl 2012-05-15 11:23:24,305 DEBUG quick_mplplots found 51.812533 days of data 2012-05-15 11:23:24,306 DEBUG quick_mplplots start day is 83.000000 2012-05-15 11:23:24,306 DEBUG quick_mplplots figures with 2.000000 days per page 2012-05-15 11:23:24,306 DEBUG quick_mplplots printing 27 pages 2012-05-15 11:23:24,306 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2012-05-15 11:23:27,489 DEBUG quick_mpl Ending plot: refl 2012-05-15 11:23:27,490 INFO quick_adcp --------------------------------------------- 2012-05-15 11:23:27,490 INFO quick_adcp step 16: find profile flags 2012-05-15 11:23:27,491 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:23:27,491 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/edit 2012-05-15 11:23:27,491 DEBUG quick_setup running python command "run_autoedit_npy" 2012-05-15 11:23:27,491 DEBUG quick_npy Starting: autoedit 2012-05-15 11:23:31,446 DEBUG pingedit wrote 87 bad bins to abadbin_tmp.asc 2012-05-15 11:23:31,593 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2012-05-15 11:23:31,594 DEBUG quick_npy Ending: autoedit 2012-05-15 11:23:31,594 INFO quick_adcp --------------------------------------------- 2012-05-15 11:23:31,594 INFO quick_adcp step 17: apply editing 2012-05-15 11:23:31,595 DEBUG quick_run starting in: /home/data/at20/proc/wh300 2012-05-15 11:23:31,595 DEBUG quick_run executing commands from: edit 2012-05-15 11:23:31,602 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/dbupdate ../adcpdb/a_at abadprf_tmp.asc 2012-05-15 11:23:31,629 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/badbin ../adcpdb/a_at abadbin_tmp.asc 2012-05-15 11:23:31,705 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/set_lgb ../adcpdb/a_at 20 2012-05-15 11:23:31,740 DEBUG quick_subs dbname: ../adcpdb/a_at pg_min: 50 set_range_bit time_ranges: all 2012-05-15 11:23:31,741 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/setflags setflags.tmp 2012-05-15 11:23:32,513 DEBUG quick_run changing directories back to /home/data/at20/proc/wh300 2012-05-15 11:23:32,514 INFO quick_adcp --------------------------------------------- 2012-05-15 11:23:32,514 INFO quick_adcp step 18: run nav steps 2012-05-15 11:23:32,514 DEBUG quick_setup nav/as_nav.tmp exists 2012-05-15 11:23:32,515 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:23:32,515 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/nav 2012-05-15 11:23:32,515 DEBUG quick_setup running python command "as_nav" 2012-05-15 11:23:32,515 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at 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 2012/03/24 13:36:32 to 2012/05/15 09:10:35 /* the whole time range */ 2012-05-15 11:23:32,516 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2012-05-15 11:23:33,760 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:23:33,760 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/nav 2012-05-15 11:23:33,761 DEBUG quick_setup running python command "refabs" 2012-05-15 11:23:33,761 DEBUG quick_subs fix_file_type: simple reference_file: a_at.nav fix_file: a_at.gps output: a_at.ref year_base= 2012 ensemble_length= 300 gap_tolerance= 10 2012-05-15 11:23:33,762 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabs refabs.tmp 2012-05-15 11:23:34,517 DEBUG quick_setup nav/smoothr.tmp exists 2012-05-15 11:23:34,517 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:23:34,517 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/nav 2012-05-15 11:23:34,518 DEBUG quick_setup running python command "smoothr" 2012-05-15 11:23:34,518 DEBUG quick_subs reference_file: a_at.nav refabs_output: a_at.ref output: a_at.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 2012-05-15 11:23:34,521 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/smoothr smoothr.tmp 2012-05-15 11:23:41,147 DEBUG quick_npy Starting: refsm 2012-05-15 11:23:44,674 DEBUG nav dtmin = -0.50 dtmax = 0.55 2012-05-15 11:23:51,004 DEBUG quick_npy Ending: refsm 2012-05-15 11:23:51,004 DEBUG quick_setup nav/putnav.tmp exists 2012-05-15 11:23:51,007 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:23:51,007 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/nav 2012-05-15 11:23:51,007 DEBUG quick_setup running python command "putnav" 2012-05-15 11:23:51,008 DEBUG quick_subs dbname: ../adcpdb/a_at position_file: a_at_refsm.asc year_base= 2012 tolerance= 5 navigation_sources: gps end 2012-05-15 11:23:51,008 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/putnav putnav.tmp 2012-05-15 11:23:52,990 DEBUG quick_mpl Starting plot: nav 2012-05-15 11:23:55,623 DEBUG quick_mpl Ending plot: nav 2012-05-15 11:23:55,623 DEBUG quick_mpl Starting plot: refl 2012-05-15 11:23:59,656 DEBUG quick_mplplots found 51.812533 days of data 2012-05-15 11:23:59,656 DEBUG quick_mplplots start day is 83.000000 2012-05-15 11:23:59,656 DEBUG quick_mplplots figures with 2.000000 days per page 2012-05-15 11:23:59,656 DEBUG quick_mplplots printing 27 pages 2012-05-15 11:23:59,656 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2012-05-15 11:24:02,840 DEBUG quick_mpl Ending plot: refl 2012-05-15 11:24:02,842 INFO quick_adcp --------------------------------------------- 2012-05-15 11:24:02,842 INFO quick_adcp step 19: plot temperature 2012-05-15 11:24:02,843 DEBUG quick_setup edit/lst_temp.tmp exists 2012-05-15 11:24:02,843 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:24:02,843 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/edit 2012-05-15 11:24:02,844 DEBUG quick_setup running python command "lst_temp" 2012-05-15 11:24:02,844 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at.tem step_size= 1 year_base= 2012 time_ranges: all 2012-05-15 11:24:02,844 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_temp lst_temp.tmp 2012-05-15 11:24:03,417 DEBUG quick_mpl Starting plot: temp 2012-05-15 11:24:04,594 DEBUG quick_mplplots plotting 37308 points 2012-05-15 11:24:05,796 DEBUG quick_mpl Ending plot: temp 2012-05-15 11:24:05,803 INFO quick_adcp --------------------------------------------- 2012-05-15 11:24:05,804 INFO quick_adcp step 20: run calibration steps 2012-05-15 11:24:05,804 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2012-05-15 11:24:05,804 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:24:05,808 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/cal/botmtrk 2012-05-15 11:24:05,808 DEBUG quick_setup running python command "lst_btrk" 2012-05-15 11:24:05,811 DEBUG quick_subs dbname: ../../adcpdb/a_at output: a_at.btm step_size= 1 year_base= 2012 time_ranges: 2012/03/24 13:36:32 to 2012/05/15 09:10:35 /* whole time range */ 2012-05-15 11:24:05,811 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_btrk lst_btrk.tmp 2012-05-15 11:24:06,186 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2012-05-15 11:24:06,187 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:24:06,187 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/cal/botmtrk 2012-05-15 11:24:06,187 DEBUG quick_setup running python command "refabsbt" 2012-05-15 11:24:06,188 DEBUG quick_subs fix_file_type: simple reference_file: a_at.btm fix_file: ../../nav/a_at.gps output: a_at.ref year_base= 2012 ensemble_length= 300 gap_tolerance= 60 2012-05-15 11:24:06,188 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabsbt refabsbt.tmp 2012-05-15 11:24:06,778 DEBUG quick_mpl Starting plot: btcal 2012-05-15 11:24:08,389 DEBUG quick_mplplots Returning from Btplot with no good output 2012-05-15 11:24:08,389 DEBUG quick_mpl Ending plot: btcal 2012-05-15 11:24:08,390 DEBUG quick_setup nav/as_nav.tmp exists 2012-05-15 11:24:08,390 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:24:08,390 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/nav 2012-05-15 11:24:08,391 DEBUG quick_setup running python command "as_nav" 2012-05-15 11:24:08,391 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at 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 2012/03/24 13:36:32 to 2012/05/15 09:10:35 /* the whole time range */ 2012-05-15 11:24:08,391 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2012-05-15 11:24:09,704 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2012-05-15 11:24:09,704 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:24:09,705 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/cal/watertrk 2012-05-15 11:24:09,705 DEBUG quick_setup running python command "timslip" 2012-05-15 11:24:09,705 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_at.gps reference_file: ../../nav/a_at.nav output_file: a_at_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 2012-05-15 11:24:09,706 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timslip timslip.tmp 2012-05-15 11:24:09,994 DEBUG quick_mpl Starting plot: wtcal 2012-05-15 11:24:10,013 DEBUG quick_mplplots Found 320 calibration points 2012-05-15 11:24:13,410 DEBUG quick_mpl Ending plot: wtcal 2012-05-15 11:24:13,410 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:24:13,410 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/cal/watertrk 2012-05-15 11:24:13,411 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2012-05-15 11:24:13,411 DEBUG quick_npy Starting: guess_xducerxy 2012-05-15 11:24:17,873 DEBUG quick_npy Ending: guess_xducerxy 2012-05-15 11:24:17,873 INFO quick_adcp --------------------------------------------- 2012-05-15 11:24:17,874 INFO quick_adcp step 21: extract matlab "allbins" 2012-05-15 11:24:17,874 DEBUG quick_asect ------------ step 18: make matlab files for plotting ------------- 2012-05-15 11:24:17,874 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:24:17,874 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/vector 2012-05-15 11:24:17,875 DEBUG quick_setup running python command "timegrid" 2012-05-15 11:24:17,875 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timegrid a_at.tmp 2012-05-15 11:24:17,897 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:24:17,897 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/vector 2012-05-15 11:24:17,897 DEBUG quick_setup running python command "as_vect" 2012-05-15 11:24:17,898 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_vect.tmp 2012-05-15 11:24:18,926 DEBUG quick_asect done making vector matfiles 2012-05-15 11:24:18,926 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:24:18,927 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/contour 2012-05-15 11:24:18,927 DEBUG quick_setup running python command "timegrid" 2012-05-15 11:24:18,927 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timegrid a_at.tmp 2012-05-15 11:24:18,974 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:24:18,975 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/contour 2012-05-15 11:24:18,975 DEBUG quick_setup running python command "as_cont" 2012-05-15 11:24:18,975 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_cont.tmp 2012-05-15 11:24:21,538 DEBUG quick_setup starting in /home/data/at20/proc/wh300 2012-05-15 11:24:21,539 DEBUG quick_setup executing commands from /home/data/at20/proc/wh300/contour 2012-05-15 11:24:21,539 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_at 2012-05-15 11:24:26,896 DEBUG quick_asect done running getmat with "allbins" 2012-05-15 11:24:26,897 INFO quick_adcp --------------------------------------------- 2012-05-15 11:24:26,897 INFO quick_adcp step 22: write "cruise_info.txt" 2012-05-15 11:24:27,062 INFO root copying NOFIG to /home/adcp/www/figures/wh300_hcorr_plot.png 2012-05-15 11:24:27,064 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/wh300_hcorr_plot_thumb.png 2012-05-15 11:24:27,065 DEBUG root matfile is contour/contour_uv.mat 2012-05-15 11:24:27,685 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/wh300_cont_uv.mat 2012-05-15 11:24:27,685 DEBUG root matfile is vector/vector_uv.mat 2012-05-15 11:24:27,686 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/wh300_vect_uv.mat 2012-05-15 11:24:27,687 DEBUG root matfile is contour/contour_xy.mat 2012-05-15 11:24:27,688 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/wh300_cont_xy.mat 2012-05-15 11:24:27,688 DEBUG root matfile is vector/vector_xy.mat 2012-05-15 11:24:27,697 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/wh300_vect_xy.mat 2012-05-15 11:24:27,698 DEBUG root about to copy file edit/a_at.tem to /home/adcp/www/data/wh300_temp.asc 2012-05-15 11:24:27,712 INFO root copying edit/a_at.tem to /home/adcp/www/data/wh300_temp.asc 2012-05-15 11:24:38,936 DEBUG root about to copy netcdf file /home/data/at20/proc/wh300/contour/wh300.nc to /home/adcp/www/data/wh300.nc 2012-05-15 11:24:39,051 INFO root copying edit/a_at.tem to /home/adcp/www/data/wh300.nc 2012-05-15 11:24:39,756 INFO root generating pingstats for wh300 2012-05-15 11:24:39,757 INFO root Ending quick_adcp.py