2016-10-02 17:08:19,645 DEBUG root about to write control file parameters to --yearbase 2016 --cruisename SR1606 --configtype python --sonar wh300 --dbname a_sr --datatype uhdas --cfgpath /home/data/SR1606/proc/wh300/config --ens_len 120 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea #offset between transducer and gps, applied in at-sea processing # NOTE : read special instructions to change offsets # diagnostics in cal/watertrk/guess_xducerxy.out # parameters used: --xducer_dx 0 --xducer_dy 0 ## see config/SR1606_proc.py for other settings --skip_avg ## see above --max_search_depth 500 --ping_headcorr --proc_engine python --refuv_smoothwin 3 --incremental --find_pflags --top_plotbin 1 --auto 2016-10-02 17:08:19,645 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d wh300 2016-10-02 17:08:19,647 DEBUG quick_setup found cruise_info.hcorr (seapath, sea, 0) 2016-10-02 17:08:19,647 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2016-10-02 17:08:19,648 INFO quick_setup fix file is a_sr.gps 2016-10-02 17:08:19,648 INFO quick_setup reflayer: ref_method = refsm 2016-10-02 17:08:19,648 INFO quick_setup reflayer: refuv_source = nav 2016-10-02 17:08:19,648 INFO quick_setup reflayer: refuv_smoothwin = 3 2016-10-02 17:08:19,648 INFO quick_adcp importing numpy version 1.8.2 2016-10-02 17:08:19,660 INFO quick_adcp importing matplotlib version 1.4.3 2016-10-02 17:08:19,815 DEBUG quick_mpl in Q_mpl 2016-10-02 17:08:19,816 INFO quick_adcp ===================================================== 2016-10-02 17:08:19,816 INFO quick_adcp ===================================================== 2016-10-02 17:08:19,816 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d wh300 2016-10-02 17:08:19,816 INFO quick_adcp cwd is /home/data/SR1606/proc/wh300 about to run these steps: - write_clearflags - scandata - avg_and_load - codaseditsetup - setflags - getnav - lst_hdg - plot_headcorr - navsteps - find_pflags - apply_edit - navsteps - lst_temp - plot_temp - lst_npings - calib - matfiles - adcpsect - refabs - smoothnav - putnav - refplots - find_pflags - codaseditsetup 2016-10-02 17:08:19,816 DEBUG quick_asect extracting matlab files for wh300 2016-10-02 17:08:19,822 DEBUG quick_setup data directory: /home/data/SR1606/raw/wh300 2016-10-02 17:08:19,822 INFO quick_setup found 26 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/SR1606/raw/wh300/*.raw" 2016-10-02 17:08:19,822 DEBUG quick_setup found 26 files from original filelist 2016-10-02 17:08:19,822 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/SR1606/raw/wh300/sr2016_273_57194.raw ... 2016-10-02 17:08:19,822 DEBUG quick_adcp Sun Oct 2 17:08:19 2016 running quick_adcp.py as follows: --cntfile /home/data/SR1606/proc/wh300/wh300_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_sr dbpath ../adcpdb deeper_boundaries [40, 60, 80, 100, 120] firstdepth 10 gridnum 80 increment 2 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2016 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 bl_half_width 3 btrk_step 1.5 cfgpath /home/data/SR1606/proc/wh300/config cntfile /home/data/SR1606/proc/wh300/wh300_qpy.cnt commands None configtype python cruisename SR1606 data_def vmadcp.def datadir /home/data/SR1606/raw/wh300 datafile_glob *.raw datatype uhdas dbname a_sr dday_bailout None debug False ens_len 120 expert None filelist ['/home/data/SR1606/raw/wh300/sr2016_273_57194.raw', '/home/data/SR1606/raw/wh300/sr2016_273_57600.raw', '/home/data/SR1606/raw/wh300/sr2016_273_64800.raw', '/home/data/SR1606/raw/wh300/sr2016_273_72000.raw', '/home/data/SR1606/raw/wh300/sr2016_273_79200.raw', '/home/data/SR1606/raw/wh300/sr2016_274_00000.raw', '/home/data/SR1606/raw/wh300/sr2016_274_07200.raw', '/home/data/SR1606/raw/wh300/sr2016_274_14400.raw', '/home/data/SR1606/raw/wh300/sr2016_274_21600.raw', '/home/data/SR1606/raw/wh300/sr2016_274_28800.raw', '/home/data/SR1606/raw/wh300/sr2016_274_36000.raw', '/home/data/SR1606/raw/wh300/sr2016_274_43200.raw', '/home/data/SR1606/raw/wh300/sr2016_274_50400.raw', '/home/data/SR1606/raw/wh300/sr2016_274_57600.raw', '/home/data/SR1606/raw/wh300/sr2016_274_64800.raw', '/home/data/SR1606/raw/wh300/sr2016_274_72000.raw', '/home/data/SR1606/raw/wh300/sr2016_274_79200.raw', '/home/data/SR1606/raw/wh300/sr2016_275_00000.raw', '/home/data/SR1606/raw/wh300/sr2016_275_07200.raw', '/home/data/SR1606/raw/wh300/sr2016_275_14400.raw', '/home/data/SR1606/raw/wh300/sr2016_275_21600.raw', '/home/data/SR1606/raw/wh300/sr2016_275_28800.raw', '/home/data/SR1606/raw/wh300/sr2016_275_36000.raw', '/home/data/SR1606/raw/wh300/sr2016_275_43200.raw', '/home/data/SR1606/raw/wh300/sr2016_275_50400.raw', '/home/data/SR1606/raw/wh300/sr2016_275_57600.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 10 fixfile a_sr.gps fixfilexy a_sr.agt frequency 300 hcorr_inst seapath help False incremental True instname wh300 jitter 15 max_BLKprofiles 300 max_search_depth 500 maxrunsecs None min_filter_fraction 0.5 mixed_pings False model wh nosave_editcfg 0 numbins 128 pgmin 50 ping_headcorr True pingpref None pingtype bb printformats png proc_engine python proc_yearbase 2016 py_gbindirbase /home/data/SR1606/gbin ref_method refsm refuv_inputfile a_sr.gps refuv_smoothwin 3 refuv_source nav rl_endbin 20 rl_startbin 2 rotate_amplitude 1 rotate_angle 0 save_lastens 0 skip_avg True sonar wh300 steps2rerun sum_xducer_dx 0 sum_xducer_dy 0 time_angle_base ens_hcorr time_angle_file ens_hcorr.ang timeout_secs 86400 top_plotbin 1 tuv_file refsm_tuv.asc txy_file a_sr.gps ub_type 1920 uhdas_config yearbase = 2016 uhdas_dir = /home/data/SR1606 sonar = wh300 gbin = /home/data/SR1606/gbin gbinsonar = /home/data/SR1606/gbin/wh300 raw = /home/data/SR1606/raw rawsonar = /home/data/SR1606/raw/wh300 rbin = /home/data/SR1606/rbin proc = /home/data/SR1606/proc procsonar = /home/data/SR1606/proc/wh300 other attributes: gbin_params = hdg_inst : gyro hdg_inst_msgs : [('gyro', 'hdg'), ('seapath', 'sea'), ('trimble', 'hdg'), ('phins', 'hdg')] hdg_msg : hdg pitch_inst : seapath pitch_msg : sea pos_inst : seapath pos_msg : gps roll_inst : seapath roll_msg : sea hcorr = ['seapath', 'sea', 0.0] acc_heading_cutoff = 0.02 update_gbin False vardoc False varvals False wtrk_step 7 xducer_dx 0 xducer_dy 0 yearbase 2016 configured to run the following steps: write_clearflags scandata avg_and_load codaseditsetup setflags getnav lst_hdg plot_headcorr navsteps find_pflags apply_edit navsteps lst_temp plot_temp lst_npings calib matfiles adcpsect refabs smoothnav putnav refplots find_pflags codaseditsetup 2016-10-02 17:08:19,823 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:19,823 INFO quick_adcp step 1: set up files in "edit" directory 2016-10-02 17:08:19,823 INFO quick_run file exists (edit/clearflags.tmp). not writing 2016-10-02 17:08:19,823 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:19,823 INFO quick_adcp step 2: scan files for time range 2016-10-02 17:08:19,823 DEBUG quick_npy Starting: scanping 2016-10-02 17:08:19,842 DEBUG quick_npy Ending: scanping 2016-10-02 17:08:19,843 DEBUG quick_subs start_end_time 2016/09/30 16:00:00 to 2016/09/30 16:00:00 2016-10-02 17:08:19,843 DEBUG quick_subs dd0: 273.666667 dd1: 273.666667 2016-10-02 17:08:19,843 INFO quick_adcp looking for database with adcpdb/a_sr*.blk 2016-10-02 17:08:19,843 INFO quick_adcp database found: listing blocks 2016-10-02 17:08:19,843 DEBUG quick_subs removing a_srdir.blk 2016-10-02 17:08:19,844 DEBUG quick_subs about to run mkblkdir 2016-10-02 17:08:19,844 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-10-02 17:08:19,844 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-10-02 17:08:19,852 DEBUG quick_subs database passes. 2016-10-02 17:08:19,852 DEBUG quick_subs start_end_time 2016/09/30 15:55:15 to 2016/10/02 16:51:15 2016-10-02 17:08:19,852 DEBUG quick_subs dd0: 273.663368 dd1: 275.702257 2016-10-02 17:08:19,852 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2016-10-02 17:08:19,852 DEBUG quick_adcp origdb_time_range is 2016/09/30 15:55:15 to 2016/10/02 16:51:15 2016-10-02 17:08:19,852 DEBUG quick_adcp (273.663368 to 275.702257) 2016-10-02 17:08:19,852 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:19,852 INFO quick_adcp step 3: generate averaged data... 2016-10-02 17:08:19,852 INFO quick_run file load/ping_editparams.txt exists. not replacing 2016-10-02 17:08:19,852 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:19,853 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/load 2016-10-02 17:08:19,853 DEBUG quick_setup running python command "run_pingavg_npy" 2016-10-02 17:08:19,853 DEBUG quick_npy Starting: pingavg 2016-10-02 17:08:19,854 DEBUG quick_npy xducerxy is [0, 0] 2016-10-02 17:08:19,854 DEBUG quick_npy singleping editing parameters: 2016-10-02 17:08:19,854 DEBUG quick_npy bigtarget_mab_window : 11 2016-10-02 17:08:19,855 DEBUG quick_npy rl_endbin : 20 2016-10-02 17:08:19,855 DEBUG quick_npy max_search_depth : 500 2016-10-02 17:08:19,855 DEBUG quick_npy cor_cutoff : 70 2016-10-02 17:08:19,855 DEBUG quick_npy ampfilt : 40 2016-10-02 17:08:19,855 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2016-10-02 17:08:19,855 DEBUG quick_npy rl_startbin : 2 2016-10-02 17:08:19,855 DEBUG quick_npy ecutoff : 0.500000 2016-10-02 17:08:19,855 DEBUG quick_npy refavg_valcutoff : 1 2016-10-02 17:08:19,855 DEBUG quick_npy weakprof_percent : 50 2016-10-02 17:08:19,855 DEBUG quick_npy bigtarget_ampthresh : 55 2016-10-02 17:08:19,858 INFO pingavg ---------------- 2016-10-02 17:08:19,858 INFO pingavg sonar is wh300 2016-10-02 17:08:19,858 INFO pingavg Pingavg.run for time range 275.666674 to 275.713498 2016-10-02 17:08:19,858 INFO pingavg transducer offset: xducer_dx = 0.000, xducer_dy = 0.000 2016-10-02 17:08:19,858 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2016-10-02 17:08:19,859 INFO pingavg ---------------- 2016-10-02 17:08:19,874 DEBUG pingavg Chunk 1 of 1, 275.666674 to 275.713498 2016-10-02 17:08:19,874 DEBUG pingavg Nothing written 2016-10-02 17:08:19,874 DEBUG quick_npy wrote 0 averages 2016-10-02 17:08:19,874 DEBUG quick_npy Ending: pingavg 2016-10-02 17:08:19,875 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:19,875 INFO quick_adcp step 4: load averaged data (to database) 2016-10-02 17:08:19,875 DEBUG quick_subs in del_overlapping 2016-10-02 17:08:19,875 DEBUG quick_subs lastblock: 2016-10-02 17:08:19,875 DEBUG quick_subs 5 2016-10-02 17:08:19,875 DEBUG quick_subs lastcmd: 2016-10-02 17:08:19,875 DEBUG quick_subs 5 2016-10-02 17:08:19,875 DEBUG quick_subs delblks: 2016-10-02 17:08:19,875 DEBUG quick_subs [5] 2016-10-02 17:08:19,875 DEBUG quick_subs loadblks: 2016-10-02 17:08:19,875 DEBUG quick_subs [5] 2016-10-02 17:08:19,876 DEBUG quick_subs about to run mkblkdir 2016-10-02 17:08:19,876 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-10-02 17:08:19,876 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-10-02 17:08:19,884 DEBUG quick_subs database passes. 2016-10-02 17:08:19,885 DEBUG quick_subs start_end_time 2016/09/30 15:55:15 to 2016/10/02 07:53:15 2016-10-02 17:08:19,885 DEBUG quick_subs dd0: 273.663368 dd1: 275.328646 2016-10-02 17:08:19,885 DEBUG quick_run [5] 2016-10-02 17:08:19,885 DEBUG quick_run cmdlist 2016-10-02 17:08:19,885 DEBUG quick_run ['./ens_blk005.cmd'] 2016-10-02 17:08:19,887 INFO quick_run loaded time range: 2016/10/02 07:55:15 to 2016/10/02 17:07:15 2016-10-02 17:08:19,887 DEBUG quick_setup load/ldcodas.tmp exists 2016-10-02 17:08:19,887 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:19,887 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/load 2016-10-02 17:08:19,887 DEBUG quick_setup running python command "ldcodas" 2016-10-02 17:08:19,887 DEBUG quick_subs filling "thisload" timerange 2016-10-02 17:08:19,888 DEBUG quick_subs in ldcodas 2016-10-02 17:08:19,888 DEBUG quick_subs cmdlist: 2016-10-02 17:08:19,889 DEBUG quick_subs ['./ens_blk005.cmd'] 2016-10-02 17:08:19,889 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_sr DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2016 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk005.cmd 2016-10-02 17:08:19,889 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2016-10-02 17:08:19,925 INFO quick_run 6 block files present 2016-10-02 17:08:19,925 DEBUG quick_subs removing a_srdir.blk 2016-10-02 17:08:19,926 DEBUG quick_subs about to run mkblkdir 2016-10-02 17:08:19,926 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-10-02 17:08:19,926 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-10-02 17:08:19,934 DEBUG quick_subs database passes. 2016-10-02 17:08:19,934 DEBUG quick_subs start_end_time 2016/09/30 15:55:15 to 2016/10/02 17:07:15 2016-10-02 17:08:19,935 DEBUG quick_subs dd0: 273.663368 dd1: 275.713368 2016-10-02 17:08:19,935 INFO quick_adcp database time range: 2016-10-02 17:08:19,935 INFO quick_adcp 2016/09/30 15:55:15 to 2016/10/02 17:07:15 2016-10-02 17:08:19,935 INFO quick_adcp (273.663368 to 275.713368) 2016-10-02 17:08:19,935 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:19,935 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/adcpdb 2016-10-02 17:08:19,935 DEBUG quick_setup running python command "lst_conf" 2016-10-02 17:08:19,935 DEBUG quick_subs dbname: a_sr output: a_sr.cnh time_ranges: all 2016-10-02 17:08:19,935 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2016-10-02 17:08:19,945 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:19,945 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2016-10-02 17:08:19,945 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2016-10-02 17:08:19,945 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:19,945 INFO quick_adcp step 6: run setflags? 2016-10-02 17:08:19,946 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:19,946 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/edit 2016-10-02 17:08:19,946 DEBUG quick_setup running python command "write_setflags" 2016-10-02 17:08:19,946 DEBUG quick_subs dbname: ../adcpdb/a_sr pg_min: 50 set_range_bit time_ranges: all 2016-10-02 17:08:19,946 DEBUG quick_setup about to run setflags setflags.tmp 2016-10-02 17:08:19,963 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:19,963 INFO quick_adcp step 7: get navigation 2016-10-02 17:08:19,963 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:19,963 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/nav 2016-10-02 17:08:19,963 DEBUG quick_setup running python command "catnav" 2016-10-02 17:08:19,964 INFO quick_subs navigation file nav/a_sr.gps created from load/*.gps2 2016-10-02 17:08:19,965 INFO quick_subs navigation file nav/a_sr.agt created from load/*.gpst2 2016-10-02 17:08:19,966 DEBUG quick_mpl Starting plot: uvship 2016-10-02 17:08:20,310 DEBUG quick_mpl Ending plot: uvship 2016-10-02 17:08:20,310 INFO quick_run plotted uvship 2016-10-02 17:08:20,310 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:20,310 INFO quick_adcp step 8: list heading 2016-10-02 17:08:20,310 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2016-10-02 17:08:20,310 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:20,310 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/cal/rotate 2016-10-02 17:08:20,310 DEBUG quick_setup running python command "lst_hdg" 2016-10-02 17:08:20,311 DEBUG quick_subs dbname: ../../adcpdb/a_sr output: scn.hdg step_size= 1 year_base= 2016 time_ranges: all 2016-10-02 17:08:20,311 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2016-10-02 17:08:20,323 INFO quick_run ... headings extracted 2016-10-02 17:08:20,323 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:20,323 INFO quick_adcp step 9: plot heading correction 2016-10-02 17:08:20,323 DEBUG quick_run hcorr_inst is seapath 2016-10-02 17:08:20,323 DEBUG quick_mpl Starting plot: hcorr 2016-10-02 17:08:20,334 DEBUG quick_mpl found 2.050003 days of data 2016-10-02 17:08:20,334 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2016-10-02 17:08:20,334 DEBUG quick_mpl printing 1 pages 2016-10-02 17:08:20,615 DEBUG quick_mpl Ending plot: hcorr 2016-10-02 17:08:20,615 INFO quick_run plots are in cal/rotate/*png 2016-10-02 17:08:20,615 INFO quick_adcp ------------------------- 2016-10-02 17:08:20,615 INFO quick_adcp ---- running navsteps --- 2016-10-02 17:08:20,615 INFO quick_adcp ------------------------- 2016-10-02 17:08:20,615 INFO quick_adcp step 10: nav steps: run adcpsect 2016-10-02 17:08:20,615 INFO quick_adcp navstep 1 2016-10-02 17:08:20,616 DEBUG quick_setup nav/as_nav.tmp exists 2016-10-02 17:08:20,616 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:20,616 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/nav 2016-10-02 17:08:20,616 DEBUG quick_setup running python command "as_nav" 2016-10-02 17:08:20,616 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2016 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 2016/09/30 15:55:15 to 2016/10/02 17:07:15 /* the whole time range */ 2016-10-02 17:08:20,616 DEBUG quick_setup about to run adcpsect as_nav.tmp 2016-10-02 17:08:20,638 INFO quick_run ... ran adcpsect for navsteps 2016-10-02 17:08:20,638 INFO quick_adcp ------------------------- 2016-10-02 17:08:20,638 INFO quick_adcp step 11: nav steps: run refabs 2016-10-02 17:08:20,638 INFO quick_adcp navstep 2 2016-10-02 17:08:20,638 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:20,638 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/nav 2016-10-02 17:08:20,639 DEBUG quick_setup running python command "refabs" 2016-10-02 17:08:20,639 DEBUG quick_subs fix_file_type: simple reference_file: a_sr.nav fix_file: a_sr.gps output: a_sr.ref year_base= 2016 ensemble_length= 120 gap_tolerance= 10 2016-10-02 17:08:20,639 DEBUG quick_setup about to run refabs refabs.tmp 2016-10-02 17:08:20,652 INFO quick_run ... ran refabs for navsteps 2016-10-02 17:08:20,652 INFO quick_adcp ------------------------- 2016-10-02 17:08:20,652 INFO quick_adcp step 12: nav steps: run smoothr for plots 2016-10-02 17:08:20,652 INFO quick_adcp navstep 3 2016-10-02 17:08:20,652 DEBUG quick_setup nav/smoothr.tmp exists 2016-10-02 17:08:20,652 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:20,653 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/nav 2016-10-02 17:08:20,653 DEBUG quick_setup running python command "smoothr" 2016-10-02 17:08:20,653 DEBUG quick_subs reference_file: a_sr.nav refabs_output: a_sr.ref output: a_sr.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= 120 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2016-10-02 17:08:20,653 DEBUG quick_setup about to run smoothr smoothr.tmp 2016-10-02 17:08:20,726 INFO quick_run ... ran smoothr 2016-10-02 17:08:20,727 INFO quick_adcp ------------------------- 2016-10-02 17:08:20,727 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2016-10-02 17:08:20,727 INFO quick_adcp navstep 4 2016-10-02 17:08:20,727 INFO quick_run smoothing method for ship speed: refsm 2016-10-02 17:08:20,727 INFO quick_run smoothing window: 3 2016-10-02 17:08:20,727 INFO quick_run ship speed source: nav 2016-10-02 17:08:20,727 DEBUG quick_npy Starting: refsm 2016-10-02 17:08:20,809 DEBUG quick_npy Ending: refsm 2016-10-02 17:08:20,809 INFO quick_run ... shipspeed smoothing step done 2016-10-02 17:08:20,810 INFO quick_adcp ------------------------- 2016-10-02 17:08:20,810 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2016-10-02 17:08:20,810 INFO quick_adcp navstep 5 2016-10-02 17:08:20,810 DEBUG quick_setup nav/put_txy.tmp exists 2016-10-02 17:08:20,810 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:20,810 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/nav 2016-10-02 17:08:20,810 DEBUG quick_setup running python command "put_txy" 2016-10-02 17:08:20,810 DEBUG quick_subs dbname: ../adcpdb/a_sr position_file: a_sr.gps year_base= 2016 tolerance= 5 2016-10-02 17:08:20,810 DEBUG quick_setup about to run put_txy put_txy.tmp 2016-10-02 17:08:20,827 INFO quick_run ... ran put_txy 2016-10-02 17:08:20,827 DEBUG quick_setup nav/put_tuv.tmp exists 2016-10-02 17:08:20,827 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:20,828 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/nav 2016-10-02 17:08:20,828 DEBUG quick_setup running python command "put_tuv" 2016-10-02 17:08:20,828 DEBUG quick_subs dbname: ../adcpdb/a_sr shipspeed_file: refsm_tuv.asc year_base= 2016 tolerance= 5 2016-10-02 17:08:20,829 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2016-10-02 17:08:20,852 INFO quick_run ... ran put_tuv 2016-10-02 17:08:20,853 DEBUG quick_mpl Starting plot: nav 2016-10-02 17:08:21,125 DEBUG quick_mpl Ending plot: nav 2016-10-02 17:08:21,126 INFO quick_run ... made navigation plot 2016-10-02 17:08:21,126 INFO quick_adcp ------------------------- 2016-10-02 17:08:21,126 INFO quick_adcp step 15: nav steps: make reflayer plots 2016-10-02 17:08:21,126 INFO quick_adcp navstep 6 2016-10-02 17:08:21,126 DEBUG quick_mpl Starting plot: refl 2016-10-02 17:08:21,154 DEBUG quick_mpl found 2.045837 days of data 2016-10-02 17:08:21,154 DEBUG quick_mpl start day is 273.000000 2016-10-02 17:08:21,154 DEBUG quick_mpl figures with 2.000000 days per page 2016-10-02 17:08:21,154 DEBUG quick_mpl printing 2 pages 2016-10-02 17:08:21,154 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2016-10-02 17:08:21,780 DEBUG quick_mpl Ending plot: refl 2016-10-02 17:08:21,780 INFO quick_run ... made reflayer plots 2016-10-02 17:08:21,781 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:21,781 INFO quick_adcp step 10: find profile flags 2016-10-02 17:08:21,781 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:21,781 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/edit 2016-10-02 17:08:21,781 DEBUG quick_setup running python command "run_autoedit_npy" 2016-10-02 17:08:21,781 DEBUG quick_npy Starting: autoedit 2016-10-02 17:08:21,862 DEBUG pingedit wrote 110 bad bins to abadbin_tmp.asc 2016-10-02 17:08:21,865 DEBUG pingedit wrote 5 bad profiles to abadprf_tmp.asc 2016-10-02 17:08:21,865 DEBUG quick_npy Ending: autoedit 2016-10-02 17:08:21,865 INFO quick_run ... extracted files using automatic editing 2016-10-02 17:08:21,866 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:21,866 INFO quick_adcp step 11: apply editing 2016-10-02 17:08:21,866 DEBUG quick_run starting in: /home/data/SR1606/proc/wh300 2016-10-02 17:08:21,866 DEBUG quick_run executing commands from: edit 2016-10-02 17:08:21,867 DEBUG quick_run about to run dbupdate ../adcpdb/a_sr abadprf_tmp.asc 2016-10-02 17:08:21,872 DEBUG quick_run about to run badbin ../adcpdb/a_sr abadbin_tmp.asc 2016-10-02 17:08:21,881 DEBUG quick_subs dbname: ../adcpdb/a_sr pg_min: 50 set_range_bit time_ranges: all 2016-10-02 17:08:21,881 DEBUG quick_run about to run setflags setflags.tmp 2016-10-02 17:08:21,904 DEBUG quick_run changing directories back to /home/data/SR1606/proc/wh300 2016-10-02 17:08:21,904 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:21,904 INFO quick_adcp step 12: run calibration steps 2016-10-02 17:08:21,904 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2016-10-02 17:08:21,904 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:21,904 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/cal/botmtrk 2016-10-02 17:08:21,904 DEBUG quick_setup running python command "lst_btrk" 2016-10-02 17:08:21,905 DEBUG quick_subs dbname: ../../adcpdb/a_sr output: a_sr.btm step_size= 1 year_base= 2016 time_ranges: 2016/09/30 15:55:15 to 2016/10/02 17:07:15 /* whole time range */ 2016-10-02 17:08:21,905 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2016-10-02 17:08:21,914 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2016-10-02 17:08:21,914 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:21,914 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/cal/botmtrk 2016-10-02 17:08:21,914 DEBUG quick_setup running python command "refabsbt" 2016-10-02 17:08:21,914 DEBUG quick_subs fix_file_type: simple reference_file: a_sr.btm fix_file: ../../nav/a_sr.gps output: a_sr.ref year_base= 2016 ensemble_length= 120 gap_tolerance= 60 2016-10-02 17:08:21,915 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2016-10-02 17:08:21,921 INFO quick_run ...bottom track info in check cal/botmtrk 2016-10-02 17:08:21,922 DEBUG quick_mpl Starting plot: btcal 2016-10-02 17:08:21,923 DEBUG quick_mpl No data in a_sr.btm 2016-10-02 17:08:21,923 DEBUG quick_mpl Returning from Btplot with no output 2016-10-02 17:08:21,923 DEBUG quick_mpl Ending plot: btcal 2016-10-02 17:08:21,923 DEBUG quick_setup nav/as_nav.tmp exists 2016-10-02 17:08:21,923 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:21,923 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/nav 2016-10-02 17:08:21,923 DEBUG quick_setup running python command "as_nav" 2016-10-02 17:08:21,924 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2016 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 2016/09/30 15:55:15 to 2016/10/02 17:07:15 /* the whole time range */ 2016-10-02 17:08:21,924 DEBUG quick_setup about to run adcpsect as_nav.tmp 2016-10-02 17:08:21,958 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2016-10-02 17:08:21,958 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:21,958 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/cal/watertrk 2016-10-02 17:08:21,958 DEBUG quick_setup running python command "timslip" 2016-10-02 17:08:21,958 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_sr.gps reference_file: ../../nav/a_sr.nav output_file: a_sr_7.cal year_base= 2016 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 2016-10-02 17:08:21,958 DEBUG quick_setup about to run timslip timslip.tmp 2016-10-02 17:08:21,968 INFO quick_run ... watertrack info in cal/watertrk 2016-10-02 17:08:21,968 DEBUG quick_mpl Starting plot: wtcal 2016-10-02 17:08:21,970 DEBUG quick_mpl Found 10 calibration points 2016-10-02 17:08:22,673 DEBUG quick_mpl Ending plot: wtcal 2016-10-02 17:08:22,674 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:22,674 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/cal/watertrk 2016-10-02 17:08:22,674 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2016-10-02 17:08:22,674 DEBUG quick_npy Starting: guess_xducerxy 2016-10-02 17:08:22,731 DEBUG quick_npy Ending: guess_xducerxy 2016-10-02 17:08:22,731 INFO quick_run ... check cal/watertrk for estimate 2016-10-02 17:08:22,731 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:22,731 INFO quick_adcp step 13: extract and plot temperature 2016-10-02 17:08:22,731 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:22,731 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/edit 2016-10-02 17:08:22,731 DEBUG quick_setup running python command "lst_temp" 2016-10-02 17:08:22,731 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr.tem step_size= 1 year_base= 2016 time_ranges: all 2016-10-02 17:08:22,732 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2016-10-02 17:08:22,745 DEBUG quick_mpl Starting plot: temp 2016-10-02 17:08:22,755 DEBUG quick_mpl plotting 1477 points 2016-10-02 17:08:23,006 DEBUG quick_mpl Ending plot: temp 2016-10-02 17:08:23,006 INFO quick_run plotted temperature 2016-10-02 17:08:23,006 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:23,006 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2016-10-02 17:08:23,007 DEBUG quick_setup edit/lst_npings.tmp exists 2016-10-02 17:08:23,007 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:23,007 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/edit 2016-10-02 17:08:23,007 DEBUG quick_setup running python command "lst_npings" 2016-10-02 17:08:23,007 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr_npings.txt step_size= 1 year_base= 2016 time_ranges: all 2016-10-02 17:08:23,007 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2016-10-02 17:08:23,020 DEBUG quick_mpl Starting plot: npings 2016-10-02 17:08:23,029 DEBUG quick_mpl plotting 1477 points 2016-10-02 17:08:23,149 DEBUG quick_mpl Ending plot: npings 2016-10-02 17:08:23,149 INFO quick_run ... plotted number of pings per ensemble 2016-10-02 17:08:23,149 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:23,149 INFO quick_adcp step 15: extract matlab "allbins" 2016-10-02 17:08:23,149 DEBUG quick_asect step 18: make matlab files for plotting 2016-10-02 17:08:23,150 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:23,150 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/vector 2016-10-02 17:08:23,150 DEBUG quick_setup running python command "timegrid" 2016-10-02 17:08:23,150 DEBUG quick_setup about to run timegrid a_sr.tmp 2016-10-02 17:08:23,156 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:23,156 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/vector 2016-10-02 17:08:23,156 DEBUG quick_setup running python command "as_vect" 2016-10-02 17:08:23,156 DEBUG quick_setup about to run adcpsect as_vect.tmp 2016-10-02 17:08:23,181 DEBUG quick_asect done making vector matfiles 2016-10-02 17:08:23,181 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:23,181 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/contour 2016-10-02 17:08:23,181 DEBUG quick_setup running python command "timegrid" 2016-10-02 17:08:23,182 DEBUG quick_setup about to run timegrid a_sr.tmp 2016-10-02 17:08:23,188 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:23,188 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/contour 2016-10-02 17:08:23,188 DEBUG quick_setup running python command "as_cont" 2016-10-02 17:08:23,188 DEBUG quick_setup about to run adcpsect as_cont.tmp 2016-10-02 17:08:23,223 DEBUG quick_setup starting in /home/data/SR1606/proc/wh300 2016-10-02 17:08:23,224 DEBUG quick_setup executing commands from /home/data/SR1606/proc/wh300/contour 2016-10-02 17:08:23,224 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_sr 2016-10-02 17:08:23,298 DEBUG quick_asect done running getmat with "allbins" 2016-10-02 17:08:23,298 INFO quick_adcp --------------------------------------------- 2016-10-02 17:08:23,298 INFO quick_adcp writing "cruise_info.txt" 2016-10-02 17:08:23,299 INFO root copying NOFIG to /home/adcp/www/figures/wh300_hcorr_plot.png 2016-10-02 17:08:23,300 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/wh300_hcorr_plot_thumb.png 2016-10-02 17:08:23,300 DEBUG root matfile is contour/contour_uv.mat 2016-10-02 17:08:23,300 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/wh300_cont_uv.mat 2016-10-02 17:08:23,300 DEBUG root matfile is vector/vector_uv.mat 2016-10-02 17:08:23,301 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/wh300_vect_uv.mat 2016-10-02 17:08:23,301 DEBUG root matfile is contour/contour_xy.mat 2016-10-02 17:08:23,301 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/wh300_cont_xy.mat 2016-10-02 17:08:23,301 DEBUG root matfile is vector/vector_xy.mat 2016-10-02 17:08:23,301 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/wh300_vect_xy.mat 2016-10-02 17:08:23,301 DEBUG root about to copy file edit/a_sr.tem to /home/adcp/www/data/wh300_temp.asc 2016-10-02 17:08:23,301 INFO root copying edit/a_sr.tem to /home/adcp/www/data/wh300_temp.asc 2016-10-02 17:08:23,319 INFO netcdf Using scipy. 2016-10-02 17:08:23,381 DEBUG root about to copy netcdf file /home/data/SR1606/proc/wh300/contour/wh300.nc to /home/adcp/www/data/wh300.nc 2016-10-02 17:08:23,383 INFO root copying edit/a_sr.tem to /home/adcp/www/data/wh300.nc 2016-10-02 17:08:23,404 INFO root generating pingstats for wh300 2016-10-02 17:08:23,404 INFO root Ending quick_adcp.py