2013-11-14 10:57:45,691 DEBUG root about to write control file parameters to --yearbase 2013 --cruisename kn213_03 --configtype python --sonar os75nb --dbname a_kn --datatype uhdas --cfgpath /home/data/kn213_03/proc/os75nb/config --ens_len 300 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea --skip_avg ## see above --max_search_depth 2000 --proc_engine python --incremental --find_pflags --hidedisplay --top_plotbin 1 --auto 2013-11-14 10:57:45,693 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d os75nb 2013-11-14 10:57:45,696 DEBUG quick_adcp progdir = /home/currents/programs 2013-11-14 10:57:45,696 DEBUG quick_adcp binos = lnx 2013-11-14 10:57:45,714 DEBUG quick_setup found cruise_info.hcorr (phins, hdg, 0) 2013-11-14 10:57:45,714 INFO quick_setup reflayer: getting ref_method from dbinfo.txt 2013-11-14 10:57:45,732 INFO quick_setup reflayer: reference method = refsm 2013-11-14 10:57:45,732 INFO quick_setup reflayer: smoothed nav file is a_kn_refsm.asc 2013-11-14 10:57:45,735 INFO quick_adcp importing numpy 2013-11-14 10:57:45,787 INFO quick_adcp importing matplotlib 2013-11-14 10:57:46,107 DEBUG quick_mpl in Q_mpl 2013-11-14 10:57:46,108 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_ref_method 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_npings lst_temp mpltest norotate opts plotbtcal_mpl plothcorr_mpl plotnav_mpl plotnpings_mpl plotrefl_mpl plottemp_mpl plotuvship_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_lstnpings run_lsttemp run_matbincmd run_matfiles run_pingavg_npy run_plot_uvship 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_refsm_uvship_npy run_rotate run_scanbin_npy run_scandata run_scanlta_npy run_scanping_npy run_setflags run_smoothr run_updategbin run_updatepygbin run_xducerxy run_xducerxy_npy scanping setflags smoothr timegrid timslip ubprint write_codas_editdefaults write_ping_editdefaults write_timerange_file zapsetup 2013-11-14 10:57:46,108 INFO quick_adcp cwd is /home/data/kn213_03/proc/os75nb 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 - lst_npings - calib - matfiles - find_pflags 2013-11-14 10:57:46,109 INFO quick_adcp original fix file is a_kn.gps 2013-11-14 10:57:46,109 INFO quick_setup reflayer: ref_method already defined (refsm) 2013-11-14 10:57:46,109 INFO quick_setup reflayer: reference method = refsm 2013-11-14 10:57:46,109 INFO quick_setup reflayer: smoothed nav file is a_kn_refsm.asc 2013-11-14 10:57:46,109 DEBUG quick_asect extracting matlab files for os75, nb pings 2013-11-14 10:57:47,250 DEBUG quick_setup data directory: /home/data/kn213_03/raw/os75 2013-11-14 10:57:47,258 INFO quick_setup found 432 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/kn213_03/raw/os75/*.raw" 2013-11-14 10:57:47,264 DEBUG quick_setup found 432 files from original filelist 2013-11-14 10:57:47,264 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/kn213_03/raw/os75/kn2013_281_43532.raw ... 2013-11-14 10:57:47,269 DEBUG quick_adcp Thu Nov 14 10:57:47 2013 running quick_adcp.py as follows: --cntfile /home/data/kn213_03/proc/os75nb/os75nb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_kn 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 28 gridnum 80 increment 10 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2013 rl_endbin 20 rl_startbin 2 ss_string separate timegrid 60 vbasename vector ----- quick_adcp.py variables and current values ------ adjust_time 1 auto True badbeam None beamangle 30 best_loggerdday_name unix_dday best_utcdday_name dday bindir /home/currents/programs/codas3/bin/lnx binos lnx btrk_step 1 cfgpath /home/data/kn213_03/proc/os75nb/config cntfile /home/data/kn213_03/proc/os75nb/os75nb_qpy.cnt commands None configtype python cruisename kn213_03 data_def vmadcp.def datadir /home/data/kn213_03/raw/os75 datafile_glob *.raw datatype uhdas dbname a_kn 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/kn213_03/raw/os75/kn2013_281_43532.raw', '/home/data/kn213_03/raw/os75/kn2013_281_50400.raw', '/home/data/kn213_03/raw/os75/kn2013_281_57600.raw', '/home/data/kn213_03/raw/os75/kn2013_281_64800.raw', '/home/data/kn213_03/raw/os75/kn2013_281_72000.raw', '/home/data/kn213_03/raw/os75/kn2013_281_79200.raw', '/home/data/kn213_03/raw/os75/kn2013_282_00000.raw', '/home/data/kn213_03/raw/os75/kn2013_282_07200.raw', '/home/data/kn213_03/raw/os75/kn2013_282_14400.raw', '/home/data/kn213_03/raw/os75/kn2013_282_21600.raw', '/home/data/kn213_03/raw/os75/kn2013_282_28800.raw', '/home/data/kn213_03/raw/os75/kn2013_282_36000.raw', '/home/data/kn213_03/raw/os75/kn2013_282_43200.raw', 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'/home/data/kn213_03/raw/os75/kn2013_317_07200.raw', '/home/data/kn213_03/raw/os75/kn2013_317_14400.raw', '/home/data/kn213_03/raw/os75/kn2013_317_21600.raw', '/home/data/kn213_03/raw/os75/kn2013_317_28800.raw', '/home/data/kn213_03/raw/os75/kn2013_317_36000.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 28 fixfile a_kn.gps frequency 75 gbin_style python gbindirbase /home/data/kn213_03/gbin hcorr_inst phins help False hidedisplay True incremental True instname os75 jitter 15 max_BLKprofiles 300 max_search_depth 2000 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 nb post_headcorr None printformats png proc_engine python proc_yearbase 2013 progdir /home/currents/programs py_gbindirbase /home/data/kn213_03/gbin rawstd_cutoff None ref_method refsm 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_kn_refsm.asc sonar os75nb steps2rerun timeout_secs 86400 tips False tktail False top_plotbin 1 ub_type 1920 update_gbin False use_refsm False use_smoothr False use_uvship False vardoc False varvals False wtrk_step 7 xducer_dx None xducer_dy None yearbase 2013 configured to run the following steps: editsetup scandata avg_and_load setflags getnav get_headcorr rotate adcpsect refabs smoothnav putnav refplots find_pflags apply_edit navsteps lst_temp lst_npings calib matfiles find_pflags 2013-11-14 10:57:47,270 INFO quick_adcp --------------------------------------------- 2013-11-14 10:57:47,270 INFO quick_adcp step 1: set up editing files 2013-11-14 10:57:47,271 DEBUG quick_run executing commands from /home/data/kn213_03/proc/os75nb/edit 2013-11-14 10:57:47,271 DEBUG quick_run setup.m exists. not replacing 2013-11-14 10:57:47,271 DEBUG quick_run asetup.m exists. not replacing 2013-11-14 10:57:47,271 DEBUG quick_run aflagit_setup.m exists. not replacing 2013-11-14 10:57:47,272 DEBUG quick_subs dbname: ../adcpdb/a_kn pg_min: 50 clear_range /* reset range */ clear_all_bits /* clear flags except pg_min*/ clear_bad_profile /* reset access vars lgb */ time_ranges: all 2013-11-14 10:57:47,276 INFO quick_adcp --------------------------------------------- 2013-11-14 10:57:47,276 INFO quick_adcp step 2: scan files for time range 2013-11-14 10:57:47,277 INFO quick_adcp about to run numpy scan, requiring python gbins 2013-11-14 10:57:47,277 DEBUG quick_npy Starting: scanping 2013-11-14 10:57:54,077 DEBUG quick_npy Ending: scanping 2013-11-14 10:57:54,109 DEBUG quick_subs start_end_time 2013/10/09 12:05:37 to 2013/10/09 12:21:27 2013-11-14 10:57:54,109 DEBUG quick_subs dd0: 281.503900 dd1: 281.514896 2013-11-14 10:57:54,111 INFO quick_adcp in quick_adcp.py: after scan; look for database times in /home/data/kn213_03/proc/os75nb 2013-11-14 10:57:54,111 INFO quick_adcp looking for database with adcpdb/a_kn*.blk 2013-11-14 10:57:54,114 INFO quick_adcp database found: listing blocks 2013-11-14 10:57:54,170 DEBUG quick_subs removing a_kndir.blk 2013-11-14 10:57:54,171 DEBUG quick_subs about to run mkblkdir 2013-11-14 10:57:54,171 DEBUG quick_subs database still exists; rerunning mkdirblk 2013-11-14 10:57:54,172 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2013-11-14 10:57:54,290 DEBUG quick_subs database passes. 2013-11-14 10:57:54,294 DEBUG quick_subs start_end_time 2013/10/09 12:10:36 to 2013/11/14 10:40:34 2013-11-14 10:57:54,294 DEBUG quick_subs dd0: 281.507361 dd1: 317.444838 2013-11-14 10:57:54,295 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2013-11-14 10:57:54,295 DEBUG quick_adcp origdb_time_range is 2013/10/09 12:10:36 to 2013/11/14 10:40:34 2013-11-14 10:57:54,295 DEBUG quick_adcp (281.507361 to 317.444838) 2013-11-14 10:57:54,296 INFO quick_adcp --------------------------------------------- 2013-11-14 10:57:54,296 INFO quick_adcp step 3: generate averaged data... 2013-11-14 10:57:54,296 DEBUG quick_run file load/ping_editparams.txt exists. not replacing 2013-11-14 10:57:54,297 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:57:54,297 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/load 2013-11-14 10:57:54,297 DEBUG quick_setup running python command "run_pingavg_npy" 2013-11-14 10:57:54,297 DEBUG quick_npy Starting: pingavg 2013-11-14 10:57:54,322 DEBUG quick_npy singleping editing parameters: 2013-11-14 10:57:54,322 DEBUG quick_npy bigtarget_mab_window : 11 2013-11-14 10:57:54,322 DEBUG quick_npy rl_endbin : 20 2013-11-14 10:57:54,323 DEBUG quick_npy max_search_depth : 2000 2013-11-14 10:57:54,323 DEBUG quick_npy cor_cutoff : 120 2013-11-14 10:57:54,323 DEBUG quick_npy ampfilt : 40 2013-11-14 10:57:54,323 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2013-11-14 10:57:54,323 DEBUG quick_npy rl_startbin : 2 2013-11-14 10:57:54,324 DEBUG quick_npy ecutoff : 0.800000 2013-11-14 10:57:54,324 DEBUG quick_npy refavg_valcutoff : 1 2013-11-14 10:57:54,324 DEBUG quick_npy weakprof_percent : 30 2013-11-14 10:57:54,324 DEBUG quick_npy bigtarget_ampthresh : 55 2013-11-14 10:57:54,324 DEBUG quick_npy xducerxy is None 2013-11-14 10:57:54,343 INFO pingavg Pingavg.run for time range 317.416692 to 317.456651 2013-11-14 10:57:54,418 DEBUG pingavg Chunk 1 of 1, 317.416692 to 317.456651 2013-11-14 10:57:54,418 DEBUG pingavg Nothing written 2013-11-14 10:57:54,419 DEBUG quick_npy wrote 0 averages 2013-11-14 10:57:54,450 DEBUG quick_npy Ending: pingavg 2013-11-14 10:57:54,450 INFO quick_adcp --------------------------------------------- 2013-11-14 10:57:54,451 INFO quick_adcp step 4: load averaged data (to database) 2013-11-14 10:57:54,453 DEBUG quick_subs in del_overlapping 2013-11-14 10:57:54,454 DEBUG quick_subs lastblock: 2013-11-14 10:57:54,454 DEBUG quick_subs 35 2013-11-14 10:57:54,454 DEBUG quick_subs lastcmd: 2013-11-14 10:57:54,454 DEBUG quick_subs 35 2013-11-14 10:57:54,455 DEBUG quick_subs delblks: 2013-11-14 10:57:54,455 DEBUG quick_subs [35] 2013-11-14 10:57:54,455 DEBUG quick_subs loadblks: 2013-11-14 10:57:54,455 DEBUG quick_subs [35] 2013-11-14 10:57:54,457 DEBUG quick_subs about to run mkblkdir 2013-11-14 10:57:54,457 DEBUG quick_subs database still exists; rerunning mkdirblk 2013-11-14 10:57:54,458 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2013-11-14 10:57:54,492 DEBUG quick_subs database passes. 2013-11-14 10:57:54,494 DEBUG quick_subs start_end_time 2013/10/09 12:10:36 to 2013/11/13 22:05:34 2013-11-14 10:57:54,494 DEBUG quick_subs dd0: 281.507361 dd1: 316.920532 2013-11-14 10:57:54,495 DEBUG quick_run [35] 2013-11-14 10:57:54,495 DEBUG quick_run cmdlist 2013-11-14 10:57:54,495 DEBUG quick_run ['./ens_blk035.cmd'] 2013-11-14 10:57:54,600 INFO quick_run Warning: 1 files will be loaded; 35 already exist 2013-11-14 10:57:54,600 INFO quick_run Thu Nov 14 10:57:54 2013 2013-11-14 10:57:54,600 INFO quick_run about to load uhdas files 2013-11-14 10:57:54,601 INFO quick_run /home/data/kn213_03/raw/os75/kn2013_281_43532.raw /home/data/kn213_03/raw/os75/kn2013_281_50400.raw /home/data/kn213_03/raw/os75/kn2013_281_57600.raw /home/data/kn213_03/raw/os75/kn2013_281_64800.raw /home/data/kn213_03/raw/os75/kn2013_281_72000.raw ... 2013-11-14 10:57:54,601 DEBUG quick_setup load/ldcodas.tmp exists 2013-11-14 10:57:54,602 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:57:54,602 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/load 2013-11-14 10:57:54,602 DEBUG quick_setup running python command "ldcodas" 2013-11-14 10:57:54,602 DEBUG quick_subs filling "thisload" timerange 2013-11-14 10:57:54,607 DEBUG quick_subs in ldcodas 2013-11-14 10:57:54,607 DEBUG quick_subs cmdlist: 2013-11-14 10:57:54,607 DEBUG quick_subs ['./ens_blk035.cmd'] 2013-11-14 10:57:54,607 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_kn DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2013 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk035.cmd 2013-11-14 10:57:54,608 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/ldcodas ldcodas.tmp 2013-11-14 10:57:54,786 DEBUG quick_subs removing a_kndir.blk 2013-11-14 10:57:54,788 DEBUG quick_subs about to run mkblkdir 2013-11-14 10:57:54,788 DEBUG quick_subs database still exists; rerunning mkdirblk 2013-11-14 10:57:54,789 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2013-11-14 10:57:54,823 DEBUG quick_subs database passes. 2013-11-14 10:57:54,825 DEBUG quick_subs start_end_time 2013/10/09 12:10:36 to 2013/11/14 10:55:32 2013-11-14 10:57:54,825 DEBUG quick_subs dd0: 281.507361 dd1: 317.455231 2013-11-14 10:57:54,826 INFO quick_adcp --------------------- 2013-11-14 10:57:54,827 INFO quick_adcp loaded_time_range is 2013/10/09 12:10:36 to 2013/11/14 10:55:32 2013-11-14 10:57:54,827 INFO quick_adcp (281.507361 to 317.455231) 2013-11-14 10:57:54,828 INFO quick_adcp origdb_time_range is 2013/10/09 12:10:36 to 2013/11/14 10:40:34 2013-11-14 10:57:54,828 INFO quick_adcp (281.507361 to 317.444838) 2013-11-14 10:57:54,828 INFO quick_adcp thisload_time_range is 2013/11/13 22:10:34 to 2013/11/14 10:55:32 2013-11-14 10:57:54,829 INFO quick_adcp (316.924005 to 316.924005) 2013-11-14 10:57:54,829 INFO quick_adcp --------------------- 2013-11-14 10:57:54,829 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:57:54,830 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/adcpdb 2013-11-14 10:57:54,830 DEBUG quick_setup running python command "lst_conf" 2013-11-14 10:57:54,830 DEBUG quick_subs dbname: a_kn output: a_kn.cnh time_ranges: all 2013-11-14 10:57:54,831 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_conf lst_conf.tmp 2013-11-14 10:58:12,461 DEBUG quick_setup found (in edit/asetup.m): 2013-11-14 10:58:12,463 DEBUG quick_setup config.beamangle is 30 2013-11-14 10:58:12,464 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:12,465 INFO quick_adcp step 5: set up files for gautoedit.py 2013-11-14 10:58:12,467 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2013-11-14 10:58:12,468 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:12,470 INFO quick_adcp step 6: set up files for gautoedit.py 2013-11-14 10:58:12,471 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:12,472 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/edit 2013-11-14 10:58:12,474 DEBUG quick_setup running python command "setflags" 2013-11-14 10:58:12,475 DEBUG quick_subs dbname: ../adcpdb/a_kn pg_min: 50 set_range_bit time_ranges: all 2013-11-14 10:58:12,478 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/setflags setflags.tmp 2013-11-14 10:58:13,007 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:13,007 INFO quick_adcp step 7: get navigation 2013-11-14 10:58:13,008 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:13,008 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/nav 2013-11-14 10:58:13,009 DEBUG quick_setup running python command "catnav" 2013-11-14 10:58:15,361 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2013-11-14 10:58:15,362 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:15,362 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/cal/rotate 2013-11-14 10:58:15,362 DEBUG quick_setup running python command "lst_hdg" 2013-11-14 10:58:15,362 DEBUG quick_subs dbname: ../../adcpdb/a_kn output: scn.hdg step_size= 1 year_base= 2013 time_ranges: all 2013-11-14 10:58:15,363 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_hdg lst_hdg.tmp 2013-11-14 10:58:15,802 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:15,803 INFO quick_adcp step 8: get heading correction 2013-11-14 10:58:15,803 DEBUG quick_run hcorr_inst is phins 2013-11-14 10:58:15,803 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:15,804 INFO quick_adcp step 9: rotate velocities 2013-11-14 10:58:15,805 DEBUG quick_setup cal/rotate/norotate.tmp exists 2013-11-14 10:58:15,805 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:15,808 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/cal/rotate 2013-11-14 10:58:15,810 DEBUG quick_setup running python command "norotate" 2013-11-14 10:58:15,812 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_kn LOG_FILE: rotate.log TIME_RANGE: 2013/10/09 12:10:36 to 2013/11/14 10:55:32 OPTION_LIST: water_and_bottom_track: year_base= 2013 /* time_angle_file: time_angle.ang */ amplitude= 1.0 angle_0= 0.0 end end 2013-11-14 10:58:15,816 DEBUG quick_setup about to run echo "writing dummy rotate file" 2013-11-14 10:58:15,859 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:15,860 INFO quick_adcp step 10: nav steps: run adcpsect 2013-11-14 10:58:15,861 DEBUG quick_setup nav/as_nav.tmp exists 2013-11-14 10:58:15,862 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:15,863 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/nav 2013-11-14 10:58:15,863 DEBUG quick_setup running python command "as_nav" 2013-11-14 10:58:15,864 DEBUG quick_subs dbname: ../adcpdb/a_kn output: a_kn step_size: 1 ndepth: 20 time_ranges: separate year_base= 2013 option_list: pg_min= 50 navigation: reference_bins 2 to 20 end statistics: mean units= 0.01 /* cm/s instead of default m/s */ end flag_mask: ALL_BITS end end 2013/10/09 12:10:36 to 2013/11/14 10:55:32 /* the whole time range */ 2013-11-14 10:58:15,867 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2013-11-14 10:58:17,322 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:17,324 INFO quick_adcp step 11: nav steps: run refabs 2013-11-14 10:58:17,325 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:17,325 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/nav 2013-11-14 10:58:17,325 DEBUG quick_setup running python command "refabs" 2013-11-14 10:58:17,326 DEBUG quick_subs fix_file_type: simple reference_file: a_kn.nav fix_file: a_kn.gps output: a_kn.ref year_base= 2013 ensemble_length= 300 gap_tolerance= 10 2013-11-14 10:58:17,328 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabs refabs.tmp 2013-11-14 10:58:17,709 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:17,710 INFO quick_adcp step 12: nav steps: run smoothr for plots 2013-11-14 10:58:17,711 DEBUG quick_setup nav/smoothr.tmp exists 2013-11-14 10:58:17,712 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:17,712 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/nav 2013-11-14 10:58:17,713 DEBUG quick_setup running python command "smoothr" 2013-11-14 10:58:17,714 DEBUG quick_subs reference_file: a_kn.nav refabs_output: a_kn.ref output: a_kn.sm filter_hwidth= 0.0208 min_filter_fraction= 0.5 max_gap_ratio= 0.05 max_gap_distance= 50 max_gap_time= 30 /* 0.5 minutes */ ensemble_time= 300 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2013-11-14 10:58:17,715 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/smoothr smoothr.tmp 2013-11-14 10:58:19,355 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:19,356 INFO quick_adcp step 13: nav steps: smooth navigation 2013-11-14 10:58:19,357 INFO quick_adcp about to run numpy reflayer smoothing, method=refsm 2013-11-14 10:58:19,358 DEBUG quick_npy Starting: refsm 2013-11-14 10:58:21,192 DEBUG nav dtmin = -0.50 dtmax = 0.50 2013-11-14 10:58:23,394 DEBUG quick_npy Ending: refsm 2013-11-14 10:58:23,395 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:23,395 INFO quick_adcp step 14: nav steps: put smoothed nav into codasdb 2013-11-14 10:58:23,396 DEBUG quick_setup nav/putnav.tmp exists 2013-11-14 10:58:23,396 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:23,397 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/nav 2013-11-14 10:58:23,397 DEBUG quick_setup running python command "putnav" 2013-11-14 10:58:23,398 DEBUG quick_subs dbname: ../adcpdb/a_kn position_file: a_kn_refsm.asc year_base= 2013 tolerance= 5 navigation_sources: gps end 2013-11-14 10:58:23,399 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/putnav putnav.tmp 2013-11-14 10:58:23,957 INFO quick_adcp plotting navigation 2013-11-14 10:58:23,958 DEBUG quick_mpl Starting plot: nav 2013-11-14 10:58:26,879 DEBUG quick_mpl Ending plot: nav 2013-11-14 10:58:26,880 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:26,881 INFO quick_adcp step 15: nav steps: make reflayer plots 2013-11-14 10:58:26,882 DEBUG quick_mpl Starting plot: refl 2013-11-14 10:58:28,261 DEBUG quick_mplplots found 35.937485 days of data 2013-11-14 10:58:28,261 DEBUG quick_mplplots start day is 281.000000 2013-11-14 10:58:28,262 DEBUG quick_mplplots figures with 2.000000 days per page 2013-11-14 10:58:28,262 DEBUG quick_mplplots printing 19 pages 2013-11-14 10:58:28,262 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2013-11-14 10:58:32,473 DEBUG quick_mpl Ending plot: refl 2013-11-14 10:58:32,474 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:32,474 INFO quick_adcp step 16: find profile flags 2013-11-14 10:58:32,475 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:32,475 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/edit 2013-11-14 10:58:32,475 DEBUG quick_setup running python command "run_autoedit_npy" 2013-11-14 10:58:32,476 DEBUG quick_npy Starting: autoedit 2013-11-14 10:58:34,235 DEBUG pingedit wrote 62 bad bins to abadbin_tmp.asc 2013-11-14 10:58:34,333 DEBUG pingedit wrote 63 bad profiles to abadprf_tmp.asc 2013-11-14 10:58:34,334 DEBUG quick_npy Ending: autoedit 2013-11-14 10:58:34,334 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:34,334 INFO quick_adcp step 17: apply editing 2013-11-14 10:58:34,335 DEBUG quick_run starting in: /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:34,335 DEBUG quick_run executing commands from: edit 2013-11-14 10:58:34,340 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/dbupdate ../adcpdb/a_kn abadprf_tmp.asc 2013-11-14 10:58:34,385 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/badbin ../adcpdb/a_kn abadbin_tmp.asc 2013-11-14 10:58:34,451 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/set_lgb ../adcpdb/a_kn 30 2013-11-14 10:58:34,507 DEBUG quick_subs dbname: ../adcpdb/a_kn pg_min: 50 set_range_bit time_ranges: all 2013-11-14 10:58:34,509 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/setflags setflags.tmp 2013-11-14 10:58:35,074 DEBUG quick_run changing directories back to /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:35,076 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:35,077 INFO quick_adcp step 18: run nav steps 2013-11-14 10:58:35,078 DEBUG quick_setup nav/as_nav.tmp exists 2013-11-14 10:58:35,079 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:35,080 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/nav 2013-11-14 10:58:35,081 DEBUG quick_setup running python command "as_nav" 2013-11-14 10:58:35,082 DEBUG quick_subs dbname: ../adcpdb/a_kn output: a_kn step_size: 1 ndepth: 20 time_ranges: separate year_base= 2013 option_list: pg_min= 50 navigation: reference_bins 2 to 20 end statistics: mean units= 0.01 /* cm/s instead of default m/s */ end flag_mask: ALL_BITS end end 2013/10/09 12:10:36 to 2013/11/14 10:55:32 /* the whole time range */ 2013-11-14 10:58:35,084 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2013-11-14 10:58:35,798 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:35,799 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/nav 2013-11-14 10:58:35,799 DEBUG quick_setup running python command "refabs" 2013-11-14 10:58:35,800 DEBUG quick_subs fix_file_type: simple reference_file: a_kn.nav fix_file: a_kn.gps output: a_kn.ref year_base= 2013 ensemble_length= 300 gap_tolerance= 10 2013-11-14 10:58:35,801 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabs refabs.tmp 2013-11-14 10:58:36,153 DEBUG quick_setup nav/smoothr.tmp exists 2013-11-14 10:58:36,155 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:36,156 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/nav 2013-11-14 10:58:36,157 DEBUG quick_setup running python command "smoothr" 2013-11-14 10:58:36,158 DEBUG quick_subs reference_file: a_kn.nav refabs_output: a_kn.ref output: a_kn.sm filter_hwidth= 0.0208 min_filter_fraction= 0.5 max_gap_ratio= 0.05 max_gap_distance= 50 max_gap_time= 30 /* 0.5 minutes */ ensemble_time= 300 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2013-11-14 10:58:36,160 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/smoothr smoothr.tmp 2013-11-14 10:58:39,079 DEBUG quick_setup nav/putnav.tmp exists 2013-11-14 10:58:39,080 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:39,080 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/nav 2013-11-14 10:58:39,081 DEBUG quick_setup running python command "putnav" 2013-11-14 10:58:39,081 DEBUG quick_subs dbname: ../adcpdb/a_kn position_file: a_kn_refsm.asc year_base= 2013 tolerance= 5 navigation_sources: gps end 2013-11-14 10:58:39,082 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/putnav putnav.tmp 2013-11-14 10:58:39,736 DEBUG quick_mpl Starting plot: nav 2013-11-14 10:58:43,596 DEBUG quick_mpl Ending plot: nav 2013-11-14 10:58:43,597 DEBUG quick_mpl Starting plot: refl 2013-11-14 10:58:44,958 DEBUG quick_mplplots found 35.937485 days of data 2013-11-14 10:58:44,959 DEBUG quick_mplplots start day is 281.000000 2013-11-14 10:58:44,959 DEBUG quick_mplplots figures with 2.000000 days per page 2013-11-14 10:58:44,959 DEBUG quick_mplplots printing 19 pages 2013-11-14 10:58:44,959 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2013-11-14 10:58:49,811 DEBUG quick_mpl Ending plot: refl 2013-11-14 10:58:49,813 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:49,813 INFO quick_adcp step 19: plot temperature 2013-11-14 10:58:49,814 DEBUG quick_setup edit/lst_temp.tmp exists 2013-11-14 10:58:49,814 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:49,814 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/edit 2013-11-14 10:58:49,815 DEBUG quick_setup running python command "lst_temp" 2013-11-14 10:58:49,815 DEBUG quick_subs dbname: ../adcpdb/a_kn output: a_kn.tem step_size= 1 year_base= 2013 time_ranges: all 2013-11-14 10:58:49,816 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_temp lst_temp.tmp 2013-11-14 10:58:50,048 DEBUG quick_mpl Starting plot: temp 2013-11-14 10:58:50,567 DEBUG quick_mplplots plotting 10354 points 2013-11-14 10:58:51,627 DEBUG quick_mpl Ending plot: temp 2013-11-14 10:58:51,628 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:51,629 INFO quick_adcp step 20: plot numper of pings per ensemble 2013-11-14 10:58:51,629 DEBUG quick_setup edit/lst_npings.tmp exists 2013-11-14 10:58:51,629 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:51,630 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/edit 2013-11-14 10:58:51,630 DEBUG quick_setup running python command "lst_npings" 2013-11-14 10:58:51,630 DEBUG quick_subs dbname: ../adcpdb/a_kn output: a_kn_npings.txt step_size= 1 year_base= 2013 time_ranges: all 2013-11-14 10:58:51,631 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_npings lst_npings.tmp 2013-11-14 10:58:51,920 DEBUG quick_mpl Starting plot: npings 2013-11-14 10:58:52,474 DEBUG quick_mplplots plotting 10354 points 2013-11-14 10:58:53,559 DEBUG quick_mpl Ending plot: npings 2013-11-14 10:58:53,560 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:53,560 INFO quick_adcp step 21: run calibration steps 2013-11-14 10:58:53,561 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2013-11-14 10:58:53,561 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:53,562 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/cal/botmtrk 2013-11-14 10:58:53,562 DEBUG quick_setup running python command "lst_btrk" 2013-11-14 10:58:53,562 DEBUG quick_subs dbname: ../../adcpdb/a_kn output: a_kn.btm step_size= 1 year_base= 2013 time_ranges: 2013/10/09 12:10:36 to 2013/11/14 10:55:32 /* whole time range */ 2013-11-14 10:58:53,563 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_btrk lst_btrk.tmp 2013-11-14 10:58:53,668 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2013-11-14 10:58:53,669 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:53,670 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/cal/botmtrk 2013-11-14 10:58:53,670 DEBUG quick_setup running python command "refabsbt" 2013-11-14 10:58:53,670 DEBUG quick_subs fix_file_type: simple reference_file: a_kn.btm fix_file: ../../nav/a_kn.gps output: a_kn.ref year_base= 2013 ensemble_length= 300 gap_tolerance= 60 2013-11-14 10:58:53,671 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabsbt refabsbt.tmp 2013-11-14 10:58:53,688 DEBUG quick_mpl Starting plot: btcal 2013-11-14 10:58:53,691 DEBUG quick_mplplots No data in a_kn.btm 2013-11-14 10:58:53,691 DEBUG quick_mplplots Returning from Btplot with no output 2013-11-14 10:58:53,691 DEBUG quick_mpl Ending plot: btcal 2013-11-14 10:58:53,692 DEBUG quick_setup nav/as_nav.tmp exists 2013-11-14 10:58:53,692 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:53,693 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/nav 2013-11-14 10:58:53,693 DEBUG quick_setup running python command "as_nav" 2013-11-14 10:58:53,693 DEBUG quick_subs dbname: ../adcpdb/a_kn output: a_kn step_size: 1 ndepth: 20 time_ranges: separate year_base= 2013 option_list: pg_min= 50 navigation: reference_bins 2 to 20 end statistics: mean units= 0.01 /* cm/s instead of default m/s */ end flag_mask: ALL_BITS end end 2013/10/09 12:10:36 to 2013/11/14 10:55:32 /* the whole time range */ 2013-11-14 10:58:53,694 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2013-11-14 10:58:54,147 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2013-11-14 10:58:54,148 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:54,149 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/cal/watertrk 2013-11-14 10:58:54,149 DEBUG quick_setup running python command "timslip" 2013-11-14 10:58:54,150 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_kn.gps reference_file: ../../nav/a_kn.nav output_file: a_kn_7.cal year_base= 2013 min_n_fixes= 7 /* 5 7 9 */ n_refs= 7 /* 5 7 9 */ i_ref_l0= 1 i_ref_l1= 2 /* 1 2 3 */ i_ref_r0= 5 /* 4 5 6 */ i_ref_r1= 6 /* 4 6 8 */ up_thresh= 3.0 /* m/s */ down_thresh= 3.0 /* m/s */ turn_speed= 2.0 /* m/s */ turn_thresh= 60 /* degrees */ dtmax= 360 /* seconds, for 300-second ensembles */ tolerance= 5.e-5 /* days, about 5 seconds */ grid: ensemble use_shifted_times? no 2013-11-14 10:58:54,151 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timslip timslip.tmp 2013-11-14 10:58:54,277 DEBUG quick_mpl Starting plot: wtcal 2013-11-14 10:58:54,285 DEBUG quick_mplplots Found 54 calibration points 2013-11-14 10:58:58,700 DEBUG quick_mpl Ending plot: wtcal 2013-11-14 10:58:58,700 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:58:58,701 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/cal/watertrk 2013-11-14 10:58:58,701 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2013-11-14 10:58:58,701 DEBUG quick_npy Starting: guess_xducerxy 2013-11-14 10:58:59,998 DEBUG quick_npy Ending: guess_xducerxy 2013-11-14 10:58:59,998 INFO quick_adcp --------------------------------------------- 2013-11-14 10:58:59,999 INFO quick_adcp step 22: extract matlab "allbins" 2013-11-14 10:58:59,999 DEBUG quick_asect ------------ step 18: make matlab files for plotting ------------- 2013-11-14 10:58:59,999 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:59:00,000 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/vector 2013-11-14 10:59:00,000 DEBUG quick_setup running python command "timegrid" 2013-11-14 10:59:00,001 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timegrid a_kn.tmp 2013-11-14 10:59:00,044 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:59:00,046 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/vector 2013-11-14 10:59:00,046 DEBUG quick_setup running python command "as_vect" 2013-11-14 10:59:00,047 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_vect.tmp 2013-11-14 10:59:00,707 DEBUG quick_asect done making vector matfiles 2013-11-14 10:59:00,708 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:59:00,710 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/contour 2013-11-14 10:59:00,710 DEBUG quick_setup running python command "timegrid" 2013-11-14 10:59:00,712 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timegrid a_kn.tmp 2013-11-14 10:59:00,785 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:59:00,785 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/contour 2013-11-14 10:59:00,786 DEBUG quick_setup running python command "as_cont" 2013-11-14 10:59:00,787 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_cont.tmp 2013-11-14 10:59:01,620 DEBUG quick_setup starting in /home/data/kn213_03/proc/os75nb 2013-11-14 10:59:01,621 DEBUG quick_setup executing commands from /home/data/kn213_03/proc/os75nb/contour 2013-11-14 10:59:01,621 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_kn 2013-11-14 10:59:04,357 DEBUG quick_asect done running getmat with "allbins" 2013-11-14 10:59:04,358 INFO quick_adcp --------------------------------------------- 2013-11-14 10:59:04,358 INFO quick_adcp step 23: write "cruise_info.txt" 2013-11-14 10:59:04,566 INFO root copying NOFIG to /home/adcp/www/figures/os75nb_hcorr_plot.png 2013-11-14 10:59:04,568 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os75nb_hcorr_plot_thumb.png 2013-11-14 10:59:04,569 DEBUG root matfile is contour/contour_uv.mat 2013-11-14 10:59:04,601 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os75nb_cont_uv.mat 2013-11-14 10:59:04,601 DEBUG root matfile is vector/vector_uv.mat 2013-11-14 10:59:04,606 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os75nb_vect_uv.mat 2013-11-14 10:59:04,606 DEBUG root matfile is contour/contour_xy.mat 2013-11-14 10:59:04,608 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os75nb_cont_xy.mat 2013-11-14 10:59:04,608 DEBUG root matfile is vector/vector_xy.mat 2013-11-14 10:59:04,609 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os75nb_vect_xy.mat 2013-11-14 10:59:04,610 DEBUG root about to copy file edit/a_kn.tem to /home/adcp/www/data/os75nb_temp.asc 2013-11-14 10:59:04,614 INFO root copying edit/a_kn.tem to /home/adcp/www/data/os75nb_temp.asc 2013-11-14 10:59:04,751 INFO netcdf Using pupynere. 2013-11-14 10:59:06,802 DEBUG root about to copy netcdf file /home/data/kn213_03/proc/os75nb/contour/os75nb.nc to /home/adcp/www/data/os75nb.nc 2013-11-14 10:59:06,875 INFO root copying edit/a_kn.tem to /home/adcp/www/data/os75nb.nc 2013-11-14 10:59:07,156 INFO root generating pingstats for os75nb 2013-11-14 10:59:07,156 INFO root Ending quick_adcp.py