2013-11-05 11:19:49,490 DEBUG root about to write control file parameters to --yearbase 2013 --cruisename RR1315 --configtype python --sonar os75nb --dbname a_rr --datatype uhdas --cfgpath /home/data/RR1315/proc/os75nb/config --ens_len 180 #--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 2013-11-05 11:19:49,490 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d os75nb 2013-11-05 11:19:49,491 DEBUG quick_adcp progdir = /home/currents/programs 2013-11-05 11:19:49,491 DEBUG quick_adcp binos = lnx64 2013-11-05 11:19:49,493 DEBUG quick_setup found cruise_info.hcorr (ashtech, adu, 0) 2013-11-05 11:19:49,494 INFO quick_adcp importing numpy 2013-11-05 11:19:49,511 INFO quick_adcp importing matplotlib 2013-11-05 11:19:49,651 DEBUG quick_mpl in Q_mpl 2013-11-05 11:19:49,652 DEBUG quick_adcp ------processor dictionary:------ __doc__ __init__ __module__ aflagit_setup as_cont as_nav as_vect asetup catnav check_beamangle check_dbinfo check_headcorr check_opts check_uhdascfg ddtime def_qlist del_overlapping fill_thisload_timerange get_asvars get_cmd_timerange get_filelist get_nodb_times get_time_range getmat ldcodas listblocks llgrid loadping lst_btrk lst_conf lst_hdg lst_temp mpltest norotate opts plotbtcal_mpl plothcorr_mpl plotnav_mpl plotrefl_mpl plottemp_mpl plotwtcal_mpl putnav refabs refabsbt rotate rotated run_adcpsect run_applyedit run_autoedit_npy run_calc run_calib run_editsetup run_findpflags run_getheadcorr run_getnav run_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 user_defined_headfunc write_codas_editdefaults write_ping_editdefaults write_timerange_file zapsetup 2013-11-05 11:19:49,652 DEBUG quick_adcp cwd is /home/data/RR1315/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 calib matfiles find_pflags 2013-11-05 11:19:49,652 DEBUG quick_adcp original fix file is a_rr.gps 2013-11-05 11:19:49,652 DEBUG quick_adcp smoothed nav file is a_rr_refsm.asc 2013-11-05 11:19:49,652 DEBUG quick_asect extracting matlab files for os75, nb pings 2013-11-05 11:19:49,656 DEBUG quick_subs found 30 files using wildcard expansion from "/home/data/RR1315/raw/os75/*.raw" 2013-11-05 11:19:49,656 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/RR1315/raw/os75/rr2013_306_12306.raw ... 2013-11-05 11:19:49,656 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/RR1315/raw/os75/rr2013_306_12306.raw ... 2013-11-05 11:19:49,656 DEBUG quick_adcp Tue Nov 5 11:19:49 2013 running quick_adcp.py as follows: --cntfile /home/data/RR1315/proc/os75nb/os75nb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_rr 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 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/RR1315/proc/os75nb/config cntfile /home/data/RR1315/proc/os75nb/os75nb_qpy.cnt commands None configtype python cruisename RR1315 data_def vmadcp.def datadir /home/data/RR1315/raw/os75 datafile_glob *.raw datatype uhdas dbname a_rr dday_bailout None debug False diarystr diary quick_adcp.diary 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/RR1315/raw/os75/rr2013_306_12306.raw', '/home/data/RR1315/raw/os75/rr2013_306_14400.raw', '/home/data/RR1315/raw/os75/rr2013_306_21600.raw', '/home/data/RR1315/raw/os75/rr2013_306_25480.raw', '/home/data/RR1315/raw/os75/rr2013_306_28800.raw', '/home/data/RR1315/raw/os75/rr2013_306_36000.raw', '/home/data/RR1315/raw/os75/rr2013_306_43200.raw', '/home/data/RR1315/raw/os75/rr2013_306_50400.raw', '/home/data/RR1315/raw/os75/rr2013_306_57600.raw', '/home/data/RR1315/raw/os75/rr2013_306_64800.raw', '/home/data/RR1315/raw/os75/rr2013_306_72000.raw', '/home/data/RR1315/raw/os75/rr2013_306_79200.raw', '/home/data/RR1315/raw/os75/rr2013_307_00000.raw', '/home/data/RR1315/raw/os75/rr2013_307_07200.raw', '/home/data/RR1315/raw/os75/rr2013_307_14400.raw', '/home/data/RR1315/raw/os75/rr2013_307_21600.raw', '/home/data/RR1315/raw/os75/rr2013_307_28800.raw', '/home/data/RR1315/raw/os75/rr2013_307_36000.raw', '/home/data/RR1315/raw/os75/rr2013_307_43200.raw', '/home/data/RR1315/raw/os75/rr2013_307_50400.raw', '/home/data/RR1315/raw/os75/rr2013_307_57600.raw', '/home/data/RR1315/raw/os75/rr2013_307_64800.raw', '/home/data/RR1315/raw/os75/rr2013_307_72000.raw', '/home/data/RR1315/raw/os75/rr2013_307_79200.raw', '/home/data/RR1315/raw/os75/rr2013_308_00000.raw', '/home/data/RR1315/raw/os75/rr2013_308_07200.raw', '/home/data/RR1315/raw/os75/rr2013_308_14400.raw', '/home/data/RR1315/raw/os75/rr2013_308_21600.raw', '/home/data/RR1315/raw/os75/rr2013_308_28800.raw', '/home/data/RR1315/raw/os75/rr2013_308_36000.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 28 fixfile a_rr.gps frequency 75 gbin_style python gbindirbase /home/data/RR1315/gbin hcorr_inst ashtech help False hidedisplay True incremental True instname os75 jitter 15 max_BLKprofiles 399 max_search_depth 1000 maxrunsecs None min_filter_fraction 0.5 model os nosave_editcfg 0 num_persistence 24 numbins 128 orig_fixfile a_rr.gps 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/RR1315/gbin quiet False rawstd_cutoff None rl_endbin 20 rl_startbin 2 rotate_amplitude 1 rotate_angle 0 rotate_file None save_editcfg 1 save_lastens 0 setup_info False skip_avg True smfile a_rr_refsm.asc sonar os75nb 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 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 calib matfiles find_pflags 2013-11-05 11:19:49,657 DEBUG quick_run ------------ step 3 (create suitable setup files for editing) ------------- 2013-11-05 11:19:49,657 DEBUG quick_run executing commands from /home/data/RR1315/proc/os75nb/edit 2013-11-05 11:19:49,657 DEBUG quick_run setup.m exists. not replacing 2013-11-05 11:19:49,657 DEBUG quick_run asetup.m exists. not replacing 2013-11-05 11:19:49,657 DEBUG quick_run aflagit_setup.m exists. not replacing 2013-11-05 11:19:49,657 DEBUG quick_adcp about to run numpy scan, requiring python gbins 2013-11-05 11:19:49,657 DEBUG quick_npy Starting: scanping 2013-11-05 11:19:49,687 DEBUG quick_npy Ending: scanping 2013-11-05 11:19:49,688 DEBUG quick_subs start_end_time 2013/11/03 03:25:09 to 2013/11/03 03:37:19 2013-11-05 11:19:49,688 DEBUG quick_subs dd0: 306.142465 dd1: 306.150914 2013-11-05 11:19:49,689 DEBUG quick_adcp in quick_adcp.py: after scan; look for database times in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:49,689 DEBUG quick_adcp looking for database with adcpdb/a_rr*.blk 2013-11-05 11:19:49,689 DEBUG quick_adcp database found: listing blocks 2013-11-05 11:19:49,689 DEBUG quick_subs removing a_rrdir.blk 2013-11-05 11:19:49,689 DEBUG quick_subs about to run mkblkdir 2013-11-05 11:19:49,689 DEBUG quick_subs database still exists; rerunning mkdirblk 2013-11-05 11:19:49,689 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2013-11-05 11:19:49,698 DEBUG quick_subs database passes. 2013-11-05 11:19:49,698 DEBUG quick_subs start_end_time 2013/11/03 03:28:08 to 2013/11/05 11:04:07 2013-11-05 11:19:49,698 DEBUG quick_subs dd0: 306.144537 dd1: 308.461192 2013-11-05 11:19:49,698 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2013-11-05 11:19:49,698 DEBUG quick_adcp origdb_time_range is 2013/11/03 03:28:08 to 2013/11/05 11:04:07 2013-11-05 11:19:49,698 DEBUG quick_adcp (306.144537 to 308.461192) 2013-11-05 11:19:49,699 DEBUG quick_run file load/ping_editparams.txt exists. not replacing 2013-11-05 11:19:49,699 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:49,699 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/load 2013-11-05 11:19:49,699 DEBUG quick_setup running python command "run_pingavg_npy" 2013-11-05 11:19:49,699 DEBUG quick_npy Starting: pingavg 2013-11-05 11:19:49,701 DEBUG quick_npy singleping editing parameters: 2013-11-05 11:19:49,701 DEBUG quick_npy bigtarget_mab_window : 11 2013-11-05 11:19:49,701 DEBUG quick_npy rl_endbin : 20 2013-11-05 11:19:49,701 DEBUG quick_npy max_search_depth : 1000 2013-11-05 11:19:49,701 DEBUG quick_npy cor_cutoff : 120 2013-11-05 11:19:49,701 DEBUG quick_npy ampfilt : 40 2013-11-05 11:19:49,701 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2013-11-05 11:19:49,701 DEBUG quick_npy rl_startbin : 2 2013-11-05 11:19:49,701 DEBUG quick_npy ecutoff : 1 2013-11-05 11:19:49,701 DEBUG quick_npy refavg_valcutoff : 1 2013-11-05 11:19:49,701 DEBUG quick_npy weakprof_percent : 30 2013-11-05 11:19:49,701 DEBUG quick_npy bigtarget_ampthresh : 55 2013-11-05 11:19:49,705 INFO pingavg Pingavg.run for time range 308.416680 to 308.471741 2013-11-05 11:19:49,729 DEBUG pingavg Chunk 1 of 1, 308.416680 to 308.471741 2013-11-05 11:19:49,729 DEBUG pingavg Nothing written 2013-11-05 11:19:49,730 DEBUG quick_npy wrote 0 averages 2013-11-05 11:19:49,730 DEBUG quick_npy Ending: pingavg 2013-11-05 11:19:49,730 DEBUG quick_subs in del_overlapping 2013-11-05 11:19:49,730 DEBUG quick_subs lastblock: 2013-11-05 11:19:49,730 DEBUG quick_subs 4 2013-11-05 11:19:49,731 DEBUG quick_subs lastcmd: 2013-11-05 11:19:49,731 DEBUG quick_subs 4 2013-11-05 11:19:49,731 DEBUG quick_subs delblks: 2013-11-05 11:19:49,731 DEBUG quick_subs [4] 2013-11-05 11:19:49,731 DEBUG quick_subs loadblks: 2013-11-05 11:19:49,731 DEBUG quick_subs [4] 2013-11-05 11:19:49,731 DEBUG quick_subs about to run mkblkdir 2013-11-05 11:19:49,732 DEBUG quick_subs database still exists; rerunning mkdirblk 2013-11-05 11:19:49,732 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2013-11-05 11:19:49,740 DEBUG quick_subs database passes. 2013-11-05 11:19:49,740 DEBUG quick_subs start_end_time 2013/11/03 03:28:08 to 2013/11/05 00:25:07 2013-11-05 11:19:49,740 DEBUG quick_subs dd0: 306.144537 dd1: 308.017442 2013-11-05 11:19:49,740 DEBUG quick_run [4] 2013-11-05 11:19:49,740 DEBUG quick_run cmdlist 2013-11-05 11:19:49,740 DEBUG quick_run ['./ens_blk004.cmd'] 2013-11-05 11:19:49,742 INFO quick_run Warning: 1 files will be loaded; 4 already exist 2013-11-05 11:19:49,742 INFO quick_run Tue Nov 5 11:19:49 2013 2013-11-05 11:19:49,742 INFO quick_run about to load uhdas files 2013-11-05 11:19:49,742 INFO quick_run /home/data/RR1315/raw/os75/rr2013_306_12306.raw /home/data/RR1315/raw/os75/rr2013_306_14400.raw /home/data/RR1315/raw/os75/rr2013_306_21600.raw /home/data/RR1315/raw/os75/rr2013_306_25480.raw /home/data/RR1315/raw/os75/rr2013_306_28800.raw /home/data/RR1315/raw/os75/rr2013_306_36000.raw /home/data/RR1315/raw/os75/rr2013_306_43200.raw /home/data/RR1315/raw/os75/rr2013_306_50400.raw /home/data/RR1315/raw/os75/rr2013_306_57600.raw /home/data/RR1315/raw/os75/rr2013_306_64800.raw /home/data/RR1315/raw/os75/rr2013_306_72000.raw /home/data/RR1315/raw/os75/rr2013_306_79200.raw /home/data/RR1315/raw/os75/rr2013_307_00000.raw /home/data/RR1315/raw/os75/rr2013_307_07200.raw /home/data/RR1315/raw/os75/rr2013_307_14400.raw /home/data/RR1315/raw/os75/rr2013_307_21600.raw /home/data/RR1315/raw/os75/rr2013_307_28800.raw /home/data/RR1315/raw/os75/rr2013_307_36000.raw /home/data/RR1315/raw/os75/rr2013_307_43200.raw /home/data/RR1315/raw/os75/rr2013_307_50400.raw /home/data/RR1315/raw/os75/rr2013_307_57600.raw /home/data/RR1315/raw/os75/rr2013_307_64800.raw /home/data/RR1315/raw/os75/rr2013_307_72000.raw /home/data/RR1315/raw/os75/rr2013_307_79200.raw /home/data/RR1315/raw/os75/rr2013_308_00000.raw /home/data/RR1315/raw/os75/rr2013_308_07200.raw /home/data/RR1315/raw/os75/rr2013_308_14400.raw /home/data/RR1315/raw/os75/rr2013_308_21600.raw /home/data/RR1315/raw/os75/rr2013_308_28800.raw /home/data/RR1315/raw/os75/rr2013_308_36000.raw 2013-11-05 11:19:49,742 DEBUG quick_setup load/ldcodas.tmp exists 2013-11-05 11:19:49,743 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:49,743 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/load 2013-11-05 11:19:49,743 DEBUG quick_setup running python command "ldcodas" 2013-11-05 11:19:49,743 DEBUG quick_subs filling "thisload" timerange 2013-11-05 11:19:49,744 DEBUG quick_subs in ldcodas 2013-11-05 11:19:49,744 DEBUG quick_subs cmdlist: 2013-11-05 11:19:49,744 DEBUG quick_subs ['./ens_blk004.cmd'] 2013-11-05 11:19:49,744 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_rr DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2013 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk004.cmd 2013-11-05 11:19:49,744 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/ldcodas ldcodas.tmp 2013-11-05 11:19:49,773 DEBUG quick_subs removing a_rrdir.blk 2013-11-05 11:19:49,773 DEBUG quick_subs about to run mkblkdir 2013-11-05 11:19:49,773 DEBUG quick_subs database still exists; rerunning mkdirblk 2013-11-05 11:19:49,773 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx64/mkblkdir mkblkdir.tmp 2013-11-05 11:19:49,781 DEBUG quick_subs database passes. 2013-11-05 11:19:49,782 DEBUG quick_subs start_end_time 2013/11/03 03:28:08 to 2013/11/05 11:19:08 2013-11-05 11:19:49,782 DEBUG quick_subs dd0: 306.144537 dd1: 308.471620 2013-11-05 11:19:49,782 INFO quick_adcp --------------------- 2013-11-05 11:19:49,782 INFO quick_adcp loaded_time_range is 2013/11/03 03:28:08 to 2013/11/05 11:19:08 2013-11-05 11:19:49,782 INFO quick_adcp (306.144537 to 308.471620) 2013-11-05 11:19:49,782 INFO quick_adcp origdb_time_range is 2013/11/03 03:28:08 to 2013/11/05 11:04:07 2013-11-05 11:19:49,783 INFO quick_adcp (306.144537 to 308.461192) 2013-11-05 11:19:49,783 INFO quick_adcp thisload_time_range is 2013/11/05 00:28:08 to 2013/11/05 11:19:08 2013-11-05 11:19:49,783 INFO quick_adcp (308.019537 to 308.019537) 2013-11-05 11:19:49,783 INFO quick_adcp --------------------- 2013-11-05 11:19:49,783 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:49,783 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/adcpdb 2013-11-05 11:19:49,783 DEBUG quick_setup running python command "lst_conf" 2013-11-05 11:19:49,783 DEBUG quick_subs dbname: a_rr output: a_rr.cnh time_ranges: all 2013-11-05 11:19:49,783 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_conf lst_conf.tmp 2013-11-05 11:19:49,823 DEBUG quick_setup found (in edit/asetup.m): 2013-11-05 11:19:49,824 DEBUG quick_setup config.beamangle is 30 2013-11-05 11:19:49,824 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2013-11-05 11:19:49,824 DEBUG quick_run ------------ step 4: run setflags ------------- 2013-11-05 11:19:49,824 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:49,824 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/edit 2013-11-05 11:19:49,824 DEBUG quick_setup running python command "setflags" 2013-11-05 11:19:49,824 DEBUG quick_subs dbname: ../adcpdb/a_rr pg_min: 50 set_range_bit time_ranges: all 2013-11-05 11:19:49,824 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2013-11-05 11:19:49,836 DEBUG quick_run ------------ step 5: get fixes from load/*.gps2 files ------------- 2013-11-05 11:19:49,836 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:49,836 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/nav 2013-11-05 11:19:49,836 DEBUG quick_setup running python command "catnav" 2013-11-05 11:19:49,837 DEBUG quick_run ------------ step 6: list heading ------------- 2013-11-05 11:19:49,837 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2013-11-05 11:19:49,837 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:49,837 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/cal/rotate 2013-11-05 11:19:49,837 DEBUG quick_setup running python command "lst_hdg" 2013-11-05 11:19:49,838 DEBUG quick_subs dbname: ../../adcpdb/a_rr output: scn.hdg step_size= 1 year_base= 2013 time_ranges: all 2013-11-05 11:19:49,838 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_hdg lst_hdg.tmp 2013-11-05 11:19:49,847 DEBUG quick_run ------------ step 6: get heading correction (if applicable) ------------- 2013-11-05 11:19:49,847 DEBUG quick_run hcorr_inst is ashtech 2013-11-05 11:19:49,847 DEBUG quick_mpl Starting plot: hcorr 2013-11-05 11:19:49,858 DEBUG quick_mplplots found 2.327081 days of data 2013-11-05 11:19:49,858 DEBUG quick_mplplots figures with 4 panels per page, 1.000000 days per panel 2013-11-05 11:19:49,859 DEBUG quick_mplplots printing 1 pages 2013-11-05 11:19:50,138 DEBUG quick_mpl Ending plot: hcorr 2013-11-05 11:19:50,138 DEBUG quick_run ------------ step 7: rotate ------------- 2013-11-05 11:19:50,138 DEBUG quick_setup cal/rotate/norotate.tmp exists 2013-11-05 11:19:50,138 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:50,138 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/cal/rotate 2013-11-05 11:19:50,138 DEBUG quick_setup running python command "norotate" 2013-11-05 11:19:50,138 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_rr LOG_FILE: rotate.log TIME_RANGE: 2013/11/03 03:28:08 to 2013/11/05 11:19:08 OPTION_LIST: water_and_bottom_track: year_base= 2013 /* time_angle_file: time_angle.ang */ amplitude= 1.0 angle_0= 0.0 end end 2013-11-05 11:19:50,139 DEBUG quick_setup about to run echo "writing dummy rotate file" 2013-11-05 11:19:50,143 DEBUG quick_run ------------ step 8: run adcpsect (for calib) ------------- 2013-11-05 11:19:50,143 DEBUG quick_setup nav/as_nav.tmp exists 2013-11-05 11:19:50,143 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:50,143 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/nav 2013-11-05 11:19:50,143 DEBUG quick_setup running python command "as_nav" 2013-11-05 11:19:50,144 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr 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 2013/11/03 03:28:08 to 2013/11/05 11:19:08 /* the whole time range */ 2013-11-05 11:19:50,144 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2013-11-05 11:19:50,160 DEBUG quick_run ------------ step 9: run refabs (for calib) ------------- 2013-11-05 11:19:50,161 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:50,161 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/nav 2013-11-05 11:19:50,161 DEBUG quick_setup running python command "refabs" 2013-11-05 11:19:50,161 DEBUG quick_subs fix_file_type: simple reference_file: a_rr.nav fix_file: a_rr.gps output: a_rr.ref year_base= 2013 ensemble_length= 300 gap_tolerance= 10 2013-11-05 11:19:50,161 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2013-11-05 11:19:50,173 DEBUG quick_run ------------ step 10: get smoothed navigation (for calib) ------------- 2013-11-05 11:19:50,174 DEBUG quick_setup nav/smoothr.tmp exists 2013-11-05 11:19:50,174 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:50,174 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/nav 2013-11-05 11:19:50,174 DEBUG quick_setup running python command "smoothr" 2013-11-05 11:19:50,174 DEBUG quick_subs reference_file: a_rr.nav refabs_output: a_rr.ref output: a_rr.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 2013-11-05 11:19:50,174 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2013-11-05 11:19:50,219 DEBUG quick_adcp about to run numpy refsm 2013-11-05 11:19:50,219 DEBUG quick_npy Starting: refsm 2013-11-05 11:19:50,252 INFO nav dtmin = -0.50 dtmax = 0.50 2013-11-05 11:19:50,287 DEBUG quick_npy Ending: refsm 2013-11-05 11:19:50,287 DEBUG quick_run ------------ step 11: put smoothed navigation back into database ------------- 2013-11-05 11:19:50,287 DEBUG quick_setup nav/putnav.tmp exists 2013-11-05 11:19:50,287 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:50,287 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/nav 2013-11-05 11:19:50,287 DEBUG quick_setup running python command "putnav" 2013-11-05 11:19:50,287 DEBUG quick_subs dbname: ../adcpdb/a_rr position_file: a_rr_refsm.asc year_base= 2013 tolerance= 5 navigation_sources: gps end 2013-11-05 11:19:50,288 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2013-11-05 11:19:50,305 DEBUG quick_adcp plotting navigation 2013-11-05 11:19:50,306 DEBUG quick_mpl Starting plot: nav 2013-11-05 11:19:50,549 DEBUG quick_mpl Ending plot: nav 2013-11-05 11:19:50,549 DEBUG quick_mpl Starting plot: refl 2013-11-05 11:19:50,574 DEBUG quick_mplplots found 2.325007 days of data 2013-11-05 11:19:50,574 DEBUG quick_mplplots start day is 306.000000 2013-11-05 11:19:50,574 DEBUG quick_mplplots figures with 2.000000 days per page 2013-11-05 11:19:50,574 DEBUG quick_mplplots printing 2 pages 2013-11-05 11:19:50,574 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2013-11-05 11:19:50,574 INFO quick_mplplots startdd is 306.0 2013-11-05 11:19:50,575 INFO quick_mplplots dt is 2.0 2013-11-05 11:19:51,109 DEBUG quick_mpl Ending plot: refl 2013-11-05 11:19:51,109 DEBUG quick_run ------------ step 13: automatically find profile flags using python ------------- 2013-11-05 11:19:51,109 DEBUG quick_run find profile flags ------------ *** ------------- 2013-11-05 11:19:51,109 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:51,109 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/edit 2013-11-05 11:19:51,109 DEBUG quick_setup running python command "run_autoedit_npy" 2013-11-05 11:19:51,109 DEBUG quick_npy Starting: autoedit 2013-11-05 11:19:51,189 DEBUG quick_npy Ending: autoedit 2013-11-05 11:19:51,189 DEBUG quick_run ------------ step 14: apply all profile flags to database ------------- 2013-11-05 11:19:51,190 DEBUG quick_run starting in: /home/data/RR1315/proc/os75nb 2013-11-05 11:19:51,190 DEBUG quick_run executing commands from: edit 2013-11-05 11:19:51,191 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/badbin ../adcpdb/a_rr abadbin_tmp.asc 2013-11-05 11:19:51,283 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/set_lgb ../adcpdb/a_rr 30 2013-11-05 11:19:51,292 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx64/setflags setflags.tmp 2013-11-05 11:19:51,312 DEBUG quick_run changing directories back to /home/data/RR1315/proc/os75nb 2013-11-05 11:19:51,312 DEBUG quick_run ------------ step 8: run adcpsect (for calib) ------------- 2013-11-05 11:19:51,312 DEBUG quick_setup nav/as_nav.tmp exists 2013-11-05 11:19:51,313 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:51,313 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/nav 2013-11-05 11:19:51,313 DEBUG quick_setup running python command "as_nav" 2013-11-05 11:19:51,313 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr 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 2013/11/03 03:28:08 to 2013/11/05 11:19:08 /* the whole time range */ 2013-11-05 11:19:51,313 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2013-11-05 11:19:51,330 DEBUG quick_run ------------ step 9: run refabs (for calib) ------------- 2013-11-05 11:19:51,330 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:51,330 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/nav 2013-11-05 11:19:51,330 DEBUG quick_setup running python command "refabs" 2013-11-05 11:19:51,330 DEBUG quick_subs fix_file_type: simple reference_file: a_rr.nav fix_file: a_rr.gps output: a_rr.ref year_base= 2013 ensemble_length= 300 gap_tolerance= 10 2013-11-05 11:19:51,330 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabs refabs.tmp 2013-11-05 11:19:51,343 DEBUG quick_run ------------ step 10: get smoothed navigation (for calib) ------------- 2013-11-05 11:19:51,344 DEBUG quick_setup nav/smoothr.tmp exists 2013-11-05 11:19:51,344 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:51,344 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/nav 2013-11-05 11:19:51,344 DEBUG quick_setup running python command "smoothr" 2013-11-05 11:19:51,344 DEBUG quick_subs reference_file: a_rr.nav refabs_output: a_rr.ref output: a_rr.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 2013-11-05 11:19:51,344 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/smoothr smoothr.tmp 2013-11-05 11:19:51,390 DEBUG quick_adcp running refsm 2013-11-05 11:19:51,390 DEBUG quick_npy Starting: refsm 2013-11-05 11:19:51,422 INFO nav dtmin = -0.50 dtmax = 0.50 2013-11-05 11:19:51,456 DEBUG quick_npy Ending: refsm 2013-11-05 11:19:51,456 DEBUG quick_run ------------ step 11: put smoothed navigation back into database ------------- 2013-11-05 11:19:51,456 DEBUG quick_setup nav/putnav.tmp exists 2013-11-05 11:19:51,457 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:51,457 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/nav 2013-11-05 11:19:51,457 DEBUG quick_setup running python command "putnav" 2013-11-05 11:19:51,457 DEBUG quick_subs dbname: ../adcpdb/a_rr position_file: a_rr_refsm.asc year_base= 2013 tolerance= 5 navigation_sources: gps end 2013-11-05 11:19:51,457 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/putnav putnav.tmp 2013-11-05 11:19:51,475 DEBUG quick_mpl Starting plot: nav 2013-11-05 11:19:51,731 DEBUG quick_mpl Ending plot: nav 2013-11-05 11:19:51,731 DEBUG quick_mpl Starting plot: refl 2013-11-05 11:19:51,756 DEBUG quick_mplplots found 2.325007 days of data 2013-11-05 11:19:51,756 DEBUG quick_mplplots start day is 306.000000 2013-11-05 11:19:51,756 DEBUG quick_mplplots figures with 2.000000 days per page 2013-11-05 11:19:51,756 DEBUG quick_mplplots printing 2 pages 2013-11-05 11:19:51,756 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2013-11-05 11:19:51,756 INFO quick_mplplots startdd is 306.0 2013-11-05 11:19:51,756 INFO quick_mplplots dt is 2.0 2013-11-05 11:19:52,292 DEBUG quick_mpl Ending plot: refl 2013-11-05 11:19:52,293 DEBUG quick_run ------------ step 16: list temperature and plot it ------------- 2013-11-05 11:19:52,293 DEBUG quick_setup edit/lst_temp.tmp exists 2013-11-05 11:19:52,293 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:52,293 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/edit 2013-11-05 11:19:52,293 DEBUG quick_setup running python command "lst_temp" 2013-11-05 11:19:52,293 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr.tem step_size= 1 year_base= 2013 time_ranges: all 2013-11-05 11:19:52,293 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_temp lst_temp.tmp 2013-11-05 11:19:52,305 DEBUG quick_mpl Starting plot: temp 2013-11-05 11:19:52,315 DEBUG quick_mplplots plotting 1118 points 2013-11-05 11:19:52,509 DEBUG quick_mpl Ending plot: temp 2013-11-05 11:19:52,509 DEBUG quick_run ------------ step 17: bottom track and watertrack calibrations ------------- 2013-11-05 11:19:52,509 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2013-11-05 11:19:52,510 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:52,510 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/cal/botmtrk 2013-11-05 11:19:52,510 DEBUG quick_setup running python command "lst_btrk" 2013-11-05 11:19:52,510 DEBUG quick_subs dbname: ../../adcpdb/a_rr output: a_rr.btm step_size= 1 year_base= 2013 time_ranges: 2013/11/03 03:28:08 to 2013/11/05 11:19:08 /* whole time range */ 2013-11-05 11:19:52,510 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/lst_btrk lst_btrk.tmp 2013-11-05 11:19:52,518 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2013-11-05 11:19:52,519 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:52,519 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/cal/botmtrk 2013-11-05 11:19:52,519 DEBUG quick_setup running python command "refabsbt" 2013-11-05 11:19:52,519 DEBUG quick_subs fix_file_type: simple reference_file: a_rr.btm fix_file: ../../nav/a_rr.gps output: a_rr.ref year_base= 2013 ensemble_length= 300 gap_tolerance= 60 2013-11-05 11:19:52,519 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/refabsbt refabsbt.tmp 2013-11-05 11:19:52,525 DEBUG quick_mpl Starting plot: btcal 2013-11-05 11:19:52,526 DEBUG quick_mplplots No data in a_rr.btm 2013-11-05 11:19:52,526 DEBUG quick_mplplots Returning from Btplot with no output 2013-11-05 11:19:52,526 DEBUG quick_mpl Ending plot: btcal 2013-11-05 11:19:52,526 DEBUG quick_setup nav/as_nav.tmp exists 2013-11-05 11:19:52,526 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:52,526 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/nav 2013-11-05 11:19:52,526 DEBUG quick_setup running python command "as_nav" 2013-11-05 11:19:52,526 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr 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 2013/11/03 03:28:08 to 2013/11/05 11:19:08 /* the whole time range */ 2013-11-05 11:19:52,526 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_nav.tmp 2013-11-05 11:19:52,542 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2013-11-05 11:19:52,543 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:52,543 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/cal/watertrk 2013-11-05 11:19:52,543 DEBUG quick_setup running python command "timslip" 2013-11-05 11:19:52,543 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_rr.gps reference_file: ../../nav/a_rr.nav output_file: a_rr_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 2013-11-05 11:19:52,543 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timslip timslip.tmp 2013-11-05 11:19:52,550 DEBUG quick_mpl Starting plot: wtcal 2013-11-05 11:19:52,551 DEBUG quick_mplplots Found 0 calibration points 2013-11-05 11:19:52,551 DEBUG quick_mplplots Only 0 valid points found; quitting 2013-11-05 11:19:52,551 DEBUG quick_mpl Ending plot: wtcal 2013-11-05 11:19:52,551 DEBUG quick_run ------------ calib: guess transducer location compared to gps ------------- 2013-11-05 11:19:52,552 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:52,552 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/cal/watertrk 2013-11-05 11:19:52,552 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2013-11-05 11:19:52,552 DEBUG quick_npy Starting: guess_xducerxy 2013-11-05 11:19:52,593 DEBUG quick_npy Ending: guess_xducerxy 2013-11-05 11:19:52,593 DEBUG quick_asect ------------ step 18: make matlab files for plotting ------------- 2013-11-05 11:19:52,593 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:52,593 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/vector 2013-11-05 11:19:52,593 DEBUG quick_setup running python command "timegrid" 2013-11-05 11:19:52,594 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_rr.tmp 2013-11-05 11:19:52,600 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:52,600 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/vector 2013-11-05 11:19:52,600 DEBUG quick_setup running python command "as_vect" 2013-11-05 11:19:52,600 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_vect.tmp 2013-11-05 11:19:52,624 DEBUG quick_asect done making vector matfiles 2013-11-05 11:19:52,624 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:52,624 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/contour 2013-11-05 11:19:52,624 DEBUG quick_setup running python command "timegrid" 2013-11-05 11:19:52,624 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/timegrid a_rr.tmp 2013-11-05 11:19:52,631 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:52,631 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/contour 2013-11-05 11:19:52,631 DEBUG quick_setup running python command "as_cont" 2013-11-05 11:19:52,631 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx64/adcpsect as_cont.tmp 2013-11-05 11:19:52,664 DEBUG quick_setup starting in /home/data/RR1315/proc/os75nb 2013-11-05 11:19:52,664 DEBUG quick_setup executing commands from /home/data/RR1315/proc/os75nb/contour 2013-11-05 11:19:52,664 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_rr 2013-11-05 11:19:52,734 DEBUG quick_asect done running getmat with "allbins" 2013-11-05 11:19:52,754 INFO root copying NOFIG to /home/adcp/www/figures/os75nb_hcorr_plot.png 2013-11-05 11:19:52,754 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os75nb_hcorr_plot_thumb.png 2013-11-05 11:19:52,755 DEBUG root matfile is contour/contour_uv.mat 2013-11-05 11:19:52,756 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os75nb_cont_uv.mat 2013-11-05 11:19:52,756 DEBUG root matfile is vector/vector_uv.mat 2013-11-05 11:19:52,756 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os75nb_vect_uv.mat 2013-11-05 11:19:52,756 DEBUG root matfile is contour/contour_xy.mat 2013-11-05 11:19:52,756 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os75nb_cont_xy.mat 2013-11-05 11:19:52,756 DEBUG root matfile is vector/vector_xy.mat 2013-11-05 11:19:52,756 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os75nb_vect_xy.mat 2013-11-05 11:19:52,756 DEBUG root about to copy file edit/a_rr.tem to /home/adcp/www/data/os75nb_temp.asc 2013-11-05 11:19:52,757 INFO root copying edit/a_rr.tem to /home/adcp/www/data/os75nb_temp.asc 2013-11-05 11:19:52,897 DEBUG root about to copy netcdf file /home/data/RR1315/proc/os75nb/contour/os75nb.nc to /home/adcp/www/data/os75nb.nc 2013-11-05 11:19:52,901 INFO root copying edit/a_rr.tem to /home/adcp/www/data/os75nb.nc 2013-11-05 11:19:52,912 INFO root generating pingstats for os75nb 2013-11-05 11:19:52,912 INFO root Ending quick_adcp.py