2017-02-05 21:12:42,161 DEBUG root about to write control file parameters to --yearbase 2017 --cruisename RR1702 --configtype python --sonar os75nb --dbname a_rr --datatype uhdas --cfgpath /home/data/RR1702/proc/os75nb/config --ens_len 180 #--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 2 --xducer_dy 30 ## see config/RR1702_proc.py for other settings --skip_avg ## see above --max_search_depth 2000 --ping_headcorr --proc_engine python --refuv_smoothwin 3 --incremental --find_pflags --top_plotbin 1 --auto 2017-02-05 21:12:42,161 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d os75nb 2017-02-05 21:12:42,162 DEBUG quick_setup found cruise_info.hcorr (seapath, sea, 0) 2017-02-05 21:12:42,162 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2017-02-05 21:12:42,163 INFO quick_setup fix file is a_rr.gps 2017-02-05 21:12:42,163 INFO quick_setup reflayer: ref_method = refsm 2017-02-05 21:12:42,163 INFO quick_setup reflayer: refuv_source = nav 2017-02-05 21:12:42,163 INFO quick_setup reflayer: refuv_smoothwin = 3 2017-02-05 21:12:42,163 INFO quick_adcp importing numpy version 1.8.2 2017-02-05 21:12:42,172 INFO quick_adcp importing matplotlib version 1.4.3 2017-02-05 21:12:42,276 DEBUG quick_mpl in Q_mpl 2017-02-05 21:12:42,277 INFO quick_adcp ===================================================== 2017-02-05 21:12:42,277 INFO quick_adcp ===================================================== 2017-02-05 21:12:42,277 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d os75nb 2017-02-05 21:12:42,277 INFO quick_adcp cwd is /home/data/RR1702/proc/os75nb 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 2017-02-05 21:12:42,277 DEBUG quick_asect extracting matlab files for os75nb 2017-02-05 21:12:42,291 DEBUG quick_setup data directory: /home/data/RR1702/raw/os75 2017-02-05 21:12:42,292 INFO quick_setup found 143 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/RR1702/raw/os75/*.raw" 2017-02-05 21:12:42,293 DEBUG quick_setup found 143 files from original filelist 2017-02-05 21:12:42,293 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/RR1702/raw/os75/rr2017_017_20104.raw ... 2017-02-05 21:12:42,293 DEBUG quick_adcp Sun Feb 5 21:12:42 2017 running quick_adcp.py as follows: --cntfile /home/data/RR1702/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 2017 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 bl_half_width 3 btrk_step 1.5 cfgpath /home/data/RR1702/proc/os75nb/config cntfile /home/data/RR1702/proc/os75nb/os75nb_qpy.cnt commands None configtype python cruisename RR1702 data_def vmadcp.def data_filelist None datadir /home/data/RR1702/raw/os75 datafile_glob *.raw datatype uhdas dbname a_rr dday_bailout None debug False ens_len 180 expert None filelist ['/home/data/RR1702/raw/os75/rr2017_017_20104.raw', '/home/data/RR1702/raw/os75/rr2017_017_21600.raw', 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'/home/data/RR1702/raw/os75/rr2017_033_57600.raw', '/home/data/RR1702/raw/os75/rr2017_033_64800.raw', '/home/data/RR1702/raw/os75/rr2017_033_72000.raw', '/home/data/RR1702/raw/os75/rr2017_033_79200.raw', '/home/data/RR1702/raw/os75/rr2017_034_00000.raw', '/home/data/RR1702/raw/os75/rr2017_034_07200.raw', '/home/data/RR1702/raw/os75/rr2017_034_14400.raw', '/home/data/RR1702/raw/os75/rr2017_034_21600.raw', '/home/data/RR1702/raw/os75/rr2017_034_28800.raw', '/home/data/RR1702/raw/os75/rr2017_034_36000.raw', '/home/data/RR1702/raw/os75/rr2017_034_43200.raw', '/home/data/RR1702/raw/os75/rr2017_034_50400.raw', '/home/data/RR1702/raw/os75/rr2017_034_57600.raw', '/home/data/RR1702/raw/os75/rr2017_034_64800.raw', '/home/data/RR1702/raw/os75/rr2017_034_72000.raw', '/home/data/RR1702/raw/os75/rr2017_034_79200.raw', '/home/data/RR1702/raw/os75/rr2017_035_00000.raw', '/home/data/RR1702/raw/os75/rr2017_035_07200.raw', '/home/data/RR1702/raw/os75/rr2017_035_14400.raw', '/home/data/RR1702/raw/os75/rr2017_035_21600.raw', '/home/data/RR1702/raw/os75/rr2017_035_28800.raw', '/home/data/RR1702/raw/os75/rr2017_035_36000.raw', '/home/data/RR1702/raw/os75/rr2017_035_43200.raw', '/home/data/RR1702/raw/os75/rr2017_035_50400.raw', '/home/data/RR1702/raw/os75/rr2017_035_57600.raw', '/home/data/RR1702/raw/os75/rr2017_035_64800.raw', '/home/data/RR1702/raw/os75/rr2017_035_72000.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 28 fixfile a_rr.gps fixfilexy a_rr.agt frequency 75 hcorr_inst seapath help False incremental True instname os75 jitter 15 max_BLKprofiles 300 max_search_depth 2000 maxrunsecs None min_filter_fraction 0.5 mixed_pings False model os nosave_editcfg 0 numbins 128 pgmin 50 ping_headcorr True pingpref None pingtype nb printformats png proc_engine python proc_yearbase 2017 py_gbindirbase /home/data/RR1702/gbin ref_method refsm refuv_inputfile a_rr.agt 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 os75nb steps2rerun sum_xducer_dx 2 sum_xducer_dy 30 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_rr.agt ub_type 1920 uhdas_config yearbase = 2017 uhdas_dir = /home/data/RR1702 sonar = os75nb gbin = /home/data/RR1702/gbin gbinsonar = /home/data/RR1702/gbin/os75 raw = /home/data/RR1702/raw rawsonar = /home/data/RR1702/raw/os75 rbin = /home/data/RR1702/rbin proc = /home/data/RR1702/proc procsonar = /home/data/RR1702/proc/os75nb other attributes: gbin_params = hdg_inst : phins3 hdg_inst_msgs : [('phins3', 'hdg'), ('seapath', 'sea'), ('ashtech', 'adu')] hdg_msg : hdg pitch_inst : seapath pitch_msg : sea pos_inst : gpsnav 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 2 xducer_dy 30 yearbase 2017 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 2017-02-05 21:12:42,293 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:42,293 INFO quick_adcp step 1: set up files in "edit" directory 2017-02-05 21:12:42,293 INFO quick_run file exists (edit/clearflags.tmp). not writing 2017-02-05 21:12:42,293 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:42,293 INFO quick_adcp step 2: scan files for time range 2017-02-05 21:12:42,293 DEBUG quick_npy Starting: scanping 2017-02-05 21:12:42,388 DEBUG quick_npy Ending: scanping 2017-02-05 21:12:42,389 DEBUG quick_subs start_end_time 2017/01/18 05:35:07 to 2017/01/18 05:50:17 2017-02-05 21:12:42,389 DEBUG quick_subs dd0: 17.232720 dd1: 17.243252 2017-02-05 21:12:42,389 INFO quick_adcp looking for database with adcpdb/a_rr*.blk 2017-02-05 21:12:42,389 INFO quick_adcp database found: listing blocks 2017-02-05 21:12:42,389 DEBUG quick_subs removing a_rrdir.blk 2017-02-05 21:12:42,390 DEBUG quick_subs about to run mkblkdir 2017-02-05 21:12:42,390 DEBUG quick_subs database still exists; rerunning mkdirblk 2017-02-05 21:12:42,390 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2017-02-05 21:12:42,396 DEBUG quick_subs database passes. 2017-02-05 21:12:42,397 DEBUG quick_subs start_end_time 2017/01/18 05:38:06 to 2017/02/05 20:56:56 2017-02-05 21:12:42,397 DEBUG quick_subs dd0: 17.234792 dd1: 35.872870 2017-02-05 21:12:42,397 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2017-02-05 21:12:42,397 DEBUG quick_adcp origdb_time_range is 2017/01/18 05:38:06 to 2017/02/05 20:56:56 2017-02-05 21:12:42,397 DEBUG quick_adcp (17.234792 to 35.872870) 2017-02-05 21:12:42,397 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:42,397 INFO quick_adcp step 3: generate averaged data... 2017-02-05 21:12:42,397 INFO quick_run file load/ping_editparams.txt exists. not replacing 2017-02-05 21:12:42,397 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:42,397 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/load 2017-02-05 21:12:42,397 DEBUG quick_setup running python command "run_pingavg_npy" 2017-02-05 21:12:42,397 DEBUG quick_npy Starting: pingavg 2017-02-05 21:12:42,399 DEBUG quick_npy xducerxy is [2, 30] 2017-02-05 21:12:42,399 DEBUG quick_npy singleping editing parameters: 2017-02-05 21:12:42,399 DEBUG quick_npy bigtarget_mab_window : 11 2017-02-05 21:12:42,400 DEBUG quick_npy rl_endbin : 20 2017-02-05 21:12:42,400 DEBUG quick_npy max_search_depth : 2000 2017-02-05 21:12:42,400 DEBUG quick_npy cor_cutoff : 120 2017-02-05 21:12:42,400 DEBUG quick_npy ampfilt : 40 2017-02-05 21:12:42,400 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2017-02-05 21:12:42,400 DEBUG quick_npy rl_startbin : 2 2017-02-05 21:12:42,400 DEBUG quick_npy ecutoff : 0.800000 2017-02-05 21:12:42,400 DEBUG quick_npy refavg_valcutoff : 1 2017-02-05 21:12:42,400 DEBUG quick_npy weakprof_percent : 30 2017-02-05 21:12:42,400 DEBUG quick_npy bigtarget_ampthresh : 55 2017-02-05 21:12:42,407 INFO pingavg ---------------- 2017-02-05 21:12:42,407 INFO pingavg sonar is os75nb 2017-02-05 21:12:42,407 INFO pingavg Pingavg.run for time range 35.833347 to 35.883775 2017-02-05 21:12:42,407 INFO pingavg transducer offset: xducer_dx = 2.000, xducer_dy = 30.000 2017-02-05 21:12:42,408 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2017-02-05 21:12:42,408 INFO pingavg ---------------- 2017-02-05 21:12:42,423 DEBUG pingavg Chunk 1 of 1, 35.833347 to 35.883775 2017-02-05 21:12:42,423 DEBUG pingavg Nothing written 2017-02-05 21:12:42,423 DEBUG quick_npy wrote 0 averages 2017-02-05 21:12:42,423 DEBUG quick_npy Ending: pingavg 2017-02-05 21:12:42,423 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:42,423 INFO quick_adcp step 4: load averaged data (to database) 2017-02-05 21:12:42,423 DEBUG quick_subs in del_overlapping 2017-02-05 21:12:42,424 DEBUG quick_subs lastblock: 2017-02-05 21:12:42,424 DEBUG quick_subs 21 2017-02-05 21:12:42,424 DEBUG quick_subs lastcmd: 2017-02-05 21:12:42,424 DEBUG quick_subs 21 2017-02-05 21:12:42,424 DEBUG quick_subs delblks: 2017-02-05 21:12:42,424 DEBUG quick_subs [21] 2017-02-05 21:12:42,424 DEBUG quick_subs loadblks: 2017-02-05 21:12:42,424 DEBUG quick_subs [21] 2017-02-05 21:12:42,424 DEBUG quick_subs about to run mkblkdir 2017-02-05 21:12:42,424 DEBUG quick_subs database still exists; rerunning mkdirblk 2017-02-05 21:12:42,424 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2017-02-05 21:12:42,430 DEBUG quick_subs database passes. 2017-02-05 21:12:42,431 DEBUG quick_subs start_end_time 2017/01/18 05:38:06 to 2017/02/05 10:11:56 2017-02-05 21:12:42,431 DEBUG quick_subs dd0: 17.234792 dd1: 35.424954 2017-02-05 21:12:42,431 DEBUG quick_run [21] 2017-02-05 21:12:42,431 DEBUG quick_run cmdlist 2017-02-05 21:12:42,431 DEBUG quick_run ['./ens_blk021.cmd'] 2017-02-05 21:12:42,432 INFO quick_run loaded time range: 2017/02/05 10:14:57 to 2017/02/05 21:11:55 2017-02-05 21:12:42,432 DEBUG quick_setup load/ldcodas.tmp exists 2017-02-05 21:12:42,432 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:42,432 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/load 2017-02-05 21:12:42,432 DEBUG quick_setup running python command "ldcodas" 2017-02-05 21:12:42,432 DEBUG quick_subs filling "thisload" timerange 2017-02-05 21:12:42,433 DEBUG quick_subs in ldcodas 2017-02-05 21:12:42,433 DEBUG quick_subs cmdlist: 2017-02-05 21:12:42,433 DEBUG quick_subs ['./ens_blk021.cmd'] 2017-02-05 21:12:42,433 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_rr DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2017 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk021.cmd 2017-02-05 21:12:42,433 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2017-02-05 21:12:42,454 INFO quick_run 22 block files present 2017-02-05 21:12:42,454 DEBUG quick_subs removing a_rrdir.blk 2017-02-05 21:12:42,454 DEBUG quick_subs about to run mkblkdir 2017-02-05 21:12:42,454 DEBUG quick_subs database still exists; rerunning mkdirblk 2017-02-05 21:12:42,454 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2017-02-05 21:12:42,460 DEBUG quick_subs database passes. 2017-02-05 21:12:42,461 DEBUG quick_subs start_end_time 2017/01/18 05:38:06 to 2017/02/05 21:11:55 2017-02-05 21:12:42,461 DEBUG quick_subs dd0: 17.234792 dd1: 35.883275 2017-02-05 21:12:42,461 INFO quick_adcp database time range: 2017-02-05 21:12:42,461 INFO quick_adcp 2017/01/18 05:38:06 to 2017/02/05 21:11:55 2017-02-05 21:12:42,461 INFO quick_adcp (17.234792 to 35.883275) 2017-02-05 21:12:42,461 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:42,461 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/adcpdb 2017-02-05 21:12:42,461 DEBUG quick_setup running python command "lst_conf" 2017-02-05 21:12:42,461 DEBUG quick_subs dbname: a_rr output: a_rr.cnh time_ranges: all 2017-02-05 21:12:42,461 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2017-02-05 21:12:42,478 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:42,478 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2017-02-05 21:12:42,479 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2017-02-05 21:12:42,479 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:42,479 INFO quick_adcp step 6: run setflags? 2017-02-05 21:12:42,479 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:42,479 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/edit 2017-02-05 21:12:42,479 DEBUG quick_setup running python command "write_setflags" 2017-02-05 21:12:42,479 DEBUG quick_subs dbname: ../adcpdb/a_rr pg_min: 50 set_range_bit time_ranges: all 2017-02-05 21:12:42,479 DEBUG quick_setup about to run setflags setflags.tmp 2017-02-05 21:12:42,519 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:42,519 INFO quick_adcp step 7: get navigation 2017-02-05 21:12:42,519 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:42,519 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/nav 2017-02-05 21:12:42,520 DEBUG quick_setup running python command "catnav" 2017-02-05 21:12:42,521 INFO quick_subs navigation file nav/a_rr.gps created from load/*.gps2 2017-02-05 21:12:42,522 INFO quick_subs navigation file nav/a_rr.agt created from load/*.gpst2 2017-02-05 21:12:42,524 DEBUG quick_mpl Starting plot: uvship 2017-02-05 21:12:42,799 DEBUG quick_mpl Ending plot: uvship 2017-02-05 21:12:42,799 INFO quick_run plotted uvship 2017-02-05 21:12:42,799 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:42,799 INFO quick_adcp step 8: list heading 2017-02-05 21:12:42,799 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2017-02-05 21:12:42,799 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:42,799 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/cal/rotate 2017-02-05 21:12:42,799 DEBUG quick_setup running python command "lst_hdg" 2017-02-05 21:12:42,799 DEBUG quick_subs dbname: ../../adcpdb/a_rr output: scn.hdg step_size= 1 year_base= 2017 time_ranges: all 2017-02-05 21:12:42,800 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2017-02-05 21:12:42,826 INFO quick_run ... headings extracted 2017-02-05 21:12:42,826 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:42,826 INFO quick_adcp step 9: plot heading correction 2017-02-05 21:12:42,826 DEBUG quick_run hcorr_inst is seapath 2017-02-05 21:12:42,826 DEBUG quick_mpl Starting plot: hcorr 2017-02-05 21:12:42,859 DEBUG quick_mpl found 18.648491 days of data 2017-02-05 21:12:42,859 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2017-02-05 21:12:42,859 DEBUG quick_mpl printing 5 pages 2017-02-05 21:12:43,294 DEBUG quick_mpl Ending plot: hcorr 2017-02-05 21:12:43,294 INFO quick_run plots are in cal/rotate/*png 2017-02-05 21:12:43,294 INFO quick_adcp ------------------------- 2017-02-05 21:12:43,295 INFO quick_adcp ---- running navsteps --- 2017-02-05 21:12:43,295 INFO quick_adcp ------------------------- 2017-02-05 21:12:43,295 INFO quick_adcp step 10: nav steps: run adcpsect 2017-02-05 21:12:43,295 INFO quick_adcp navstep 1 2017-02-05 21:12:43,295 DEBUG quick_setup nav/as_nav.tmp exists 2017-02-05 21:12:43,295 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:43,295 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/nav 2017-02-05 21:12:43,295 DEBUG quick_setup running python command "as_nav" 2017-02-05 21:12:43,295 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2017 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 2017/01/18 05:38:06 to 2017/02/05 21:11:55 /* the whole time range */ 2017-02-05 21:12:43,295 DEBUG quick_setup about to run adcpsect as_nav.tmp 2017-02-05 21:12:43,349 INFO quick_run ... ran adcpsect for navsteps 2017-02-05 21:12:43,349 INFO quick_adcp ------------------------- 2017-02-05 21:12:43,349 INFO quick_adcp step 11: nav steps: run refabs 2017-02-05 21:12:43,349 INFO quick_adcp navstep 2 2017-02-05 21:12:43,349 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:43,350 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/nav 2017-02-05 21:12:43,350 DEBUG quick_setup running python command "refabs" 2017-02-05 21:12:43,350 DEBUG quick_subs fix_file_type: simple reference_file: a_rr.nav fix_file: a_rr.gps output: a_rr.ref year_base= 2017 ensemble_length= 180 gap_tolerance= 10 2017-02-05 21:12:43,350 DEBUG quick_setup about to run refabs refabs.tmp 2017-02-05 21:12:43,381 INFO quick_run ... ran refabs for navsteps 2017-02-05 21:12:43,381 INFO quick_adcp ------------------------- 2017-02-05 21:12:43,381 INFO quick_adcp step 12: nav steps: run smoothr for plots 2017-02-05 21:12:43,381 INFO quick_adcp navstep 3 2017-02-05 21:12:43,381 DEBUG quick_setup nav/smoothr.tmp exists 2017-02-05 21:12:43,381 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:43,381 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/nav 2017-02-05 21:12:43,381 DEBUG quick_setup running python command "smoothr" 2017-02-05 21:12:43,381 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= 180 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2017-02-05 21:12:43,381 DEBUG quick_setup about to run smoothr smoothr.tmp 2017-02-05 21:12:43,558 INFO quick_run ... ran smoothr 2017-02-05 21:12:43,559 INFO quick_adcp ------------------------- 2017-02-05 21:12:43,559 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2017-02-05 21:12:43,559 INFO quick_adcp navstep 4 2017-02-05 21:12:43,559 INFO quick_run smoothing method for ship speed: refsm 2017-02-05 21:12:43,559 INFO quick_run smoothing window: 3 2017-02-05 21:12:43,559 INFO quick_run ship speed source: nav 2017-02-05 21:12:43,559 DEBUG quick_npy Starting: refsm 2017-02-05 21:12:43,762 DEBUG quick_npy Ending: refsm 2017-02-05 21:12:43,762 INFO quick_run ... shipspeed smoothing step done 2017-02-05 21:12:43,762 INFO quick_adcp ------------------------- 2017-02-05 21:12:43,762 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2017-02-05 21:12:43,762 INFO quick_adcp navstep 5 2017-02-05 21:12:43,762 DEBUG quick_setup nav/put_txy.tmp exists 2017-02-05 21:12:43,762 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:43,762 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/nav 2017-02-05 21:12:43,762 DEBUG quick_setup running python command "put_txy" 2017-02-05 21:12:43,763 DEBUG quick_subs dbname: ../adcpdb/a_rr position_file: a_rr.agt year_base= 2017 tolerance= 5 2017-02-05 21:12:43,763 DEBUG quick_setup about to run put_txy put_txy.tmp 2017-02-05 21:12:43,799 INFO quick_run ... ran put_txy 2017-02-05 21:12:43,799 DEBUG quick_setup nav/put_tuv.tmp exists 2017-02-05 21:12:43,799 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:43,800 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/nav 2017-02-05 21:12:43,800 DEBUG quick_setup running python command "put_tuv" 2017-02-05 21:12:43,800 DEBUG quick_subs dbname: ../adcpdb/a_rr shipspeed_file: refsm_tuv.asc year_base= 2017 tolerance= 5 2017-02-05 21:12:43,800 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2017-02-05 21:12:43,835 INFO quick_run ... ran put_tuv 2017-02-05 21:12:43,835 DEBUG quick_mpl Starting plot: nav 2017-02-05 21:12:44,072 DEBUG quick_mpl Ending plot: nav 2017-02-05 21:12:44,072 INFO quick_run ... made navigation plot 2017-02-05 21:12:44,072 INFO quick_adcp ------------------------- 2017-02-05 21:12:44,073 INFO quick_adcp step 15: nav steps: make reflayer plots 2017-02-05 21:12:44,073 INFO quick_adcp navstep 6 2017-02-05 21:12:44,073 DEBUG quick_mpl Starting plot: refl 2017-02-05 21:12:44,146 DEBUG quick_mpl found 18.642247 days of data 2017-02-05 21:12:44,146 DEBUG quick_mpl start day is 17.000000 2017-02-05 21:12:44,146 DEBUG quick_mpl figures with 2.000000 days per page 2017-02-05 21:12:44,146 DEBUG quick_mpl printing 10 pages 2017-02-05 21:12:44,146 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2017-02-05 21:12:44,576 DEBUG quick_mpl Ending plot: refl 2017-02-05 21:12:44,577 INFO quick_run ... made reflayer plots 2017-02-05 21:12:44,577 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:44,577 INFO quick_adcp step 10: find profile flags 2017-02-05 21:12:44,577 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:44,577 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/edit 2017-02-05 21:12:44,577 DEBUG quick_setup running python command "run_autoedit_npy" 2017-02-05 21:12:44,577 DEBUG quick_npy Starting: autoedit 2017-02-05 21:12:44,735 DEBUG pingedit wrote 11 bad bins to abadbin_tmp.asc 2017-02-05 21:12:44,738 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2017-02-05 21:12:44,738 DEBUG quick_npy Ending: autoedit 2017-02-05 21:12:44,738 INFO quick_run ... extracted files using automatic editing 2017-02-05 21:12:44,738 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:44,738 INFO quick_adcp step 11: apply editing 2017-02-05 21:12:44,738 DEBUG quick_run starting in: /home/data/RR1702/proc/os75nb 2017-02-05 21:12:44,738 DEBUG quick_run executing commands from: edit 2017-02-05 21:12:44,739 DEBUG quick_run about to run dbupdate ../adcpdb/a_rr abadprf_tmp.asc 2017-02-05 21:12:44,744 DEBUG quick_run about to run badbin ../adcpdb/a_rr abadbin_tmp.asc 2017-02-05 21:12:44,749 DEBUG quick_subs dbname: ../adcpdb/a_rr pg_min: 50 set_range_bit time_ranges: all 2017-02-05 21:12:44,750 DEBUG quick_run about to run setflags setflags.tmp 2017-02-05 21:12:44,800 DEBUG quick_run changing directories back to /home/data/RR1702/proc/os75nb 2017-02-05 21:12:44,800 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:44,800 INFO quick_adcp step 12: run calibration steps 2017-02-05 21:12:44,800 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2017-02-05 21:12:44,800 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:44,800 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/cal/botmtrk 2017-02-05 21:12:44,800 DEBUG quick_setup running python command "lst_btrk" 2017-02-05 21:12:44,800 DEBUG quick_subs dbname: ../../adcpdb/a_rr output: a_rr.btm step_size= 1 year_base= 2017 time_ranges: 2017/01/18 05:38:06 to 2017/02/05 21:11:55 /* whole time range */ 2017-02-05 21:12:44,800 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2017-02-05 21:12:44,821 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2017-02-05 21:12:44,821 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:44,821 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/cal/botmtrk 2017-02-05 21:12:44,821 DEBUG quick_setup running python command "refabsbt" 2017-02-05 21:12:44,821 DEBUG quick_subs fix_file_type: simple reference_file: a_rr.btm fix_file: ../../nav/a_rr.gps output: a_rr.ref year_base= 2017 ensemble_length= 180 gap_tolerance= 60 2017-02-05 21:12:44,822 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2017-02-05 21:12:44,827 INFO quick_run ...bottom track info in check cal/botmtrk 2017-02-05 21:12:44,827 DEBUG quick_mpl Starting plot: btcal 2017-02-05 21:12:44,828 DEBUG quick_mpl No data in a_rr.btm 2017-02-05 21:12:44,828 DEBUG quick_mpl Returning from Btplot with no output 2017-02-05 21:12:44,828 DEBUG quick_mpl Ending plot: btcal 2017-02-05 21:12:44,828 DEBUG quick_setup nav/as_nav.tmp exists 2017-02-05 21:12:44,828 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:44,828 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/nav 2017-02-05 21:12:44,828 DEBUG quick_setup running python command "as_nav" 2017-02-05 21:12:44,828 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2017 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 2017/01/18 05:38:06 to 2017/02/05 21:11:55 /* the whole time range */ 2017-02-05 21:12:44,828 DEBUG quick_setup about to run adcpsect as_nav.tmp 2017-02-05 21:12:44,884 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2017-02-05 21:12:44,884 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:44,884 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/cal/watertrk 2017-02-05 21:12:44,884 DEBUG quick_setup running python command "timslip" 2017-02-05 21:12:44,885 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= 2017 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 2017-02-05 21:12:44,885 DEBUG quick_setup about to run timslip timslip.tmp 2017-02-05 21:12:44,901 INFO quick_run ... watertrack info in cal/watertrk 2017-02-05 21:12:44,901 DEBUG quick_mpl Starting plot: wtcal 2017-02-05 21:12:44,903 DEBUG quick_mpl Found 22 calibration points 2017-02-05 21:12:45,434 DEBUG quick_mpl Ending plot: wtcal 2017-02-05 21:12:45,434 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:45,435 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/cal/watertrk 2017-02-05 21:12:45,435 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2017-02-05 21:12:45,435 DEBUG quick_npy Starting: guess_xducerxy 2017-02-05 21:12:45,575 DEBUG quick_npy Ending: guess_xducerxy 2017-02-05 21:12:45,575 INFO quick_run ... check cal/watertrk for estimate 2017-02-05 21:12:45,575 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:45,575 INFO quick_adcp step 13: extract and plot temperature 2017-02-05 21:12:45,575 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:45,575 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/edit 2017-02-05 21:12:45,576 DEBUG quick_setup running python command "lst_temp" 2017-02-05 21:12:45,576 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr.tem step_size= 1 year_base= 2017 time_ranges: all 2017-02-05 21:12:45,576 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2017-02-05 21:12:45,607 DEBUG quick_mpl Starting plot: temp 2017-02-05 21:12:45,632 DEBUG quick_mpl plotting 5447 points 2017-02-05 21:12:45,827 DEBUG quick_mpl Ending plot: temp 2017-02-05 21:12:45,827 INFO quick_run plotted temperature 2017-02-05 21:12:45,827 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:45,827 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2017-02-05 21:12:45,827 DEBUG quick_setup edit/lst_npings.tmp exists 2017-02-05 21:12:45,827 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:45,827 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/edit 2017-02-05 21:12:45,827 DEBUG quick_setup running python command "lst_npings" 2017-02-05 21:12:45,828 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr_npings.txt step_size= 1 year_base= 2017 time_ranges: all 2017-02-05 21:12:45,828 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2017-02-05 21:12:45,857 DEBUG quick_mpl Starting plot: npings 2017-02-05 21:12:45,881 DEBUG quick_mpl plotting 5447 points 2017-02-05 21:12:45,967 DEBUG quick_mpl Ending plot: npings 2017-02-05 21:12:45,968 INFO quick_run ... plotted number of pings per ensemble 2017-02-05 21:12:45,968 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:45,968 INFO quick_adcp step 15: extract matlab "allbins" 2017-02-05 21:12:45,968 DEBUG quick_asect step 18: make matlab files for plotting 2017-02-05 21:12:45,968 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:45,968 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/vector 2017-02-05 21:12:45,968 DEBUG quick_setup running python command "timegrid" 2017-02-05 21:12:45,968 DEBUG quick_setup about to run timegrid a_rr.tmp 2017-02-05 21:12:45,973 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:45,973 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/vector 2017-02-05 21:12:45,973 DEBUG quick_setup running python command "as_vect" 2017-02-05 21:12:45,974 DEBUG quick_setup about to run adcpsect as_vect.tmp 2017-02-05 21:12:46,048 DEBUG quick_asect done making vector matfiles 2017-02-05 21:12:46,048 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:46,048 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/contour 2017-02-05 21:12:46,048 DEBUG quick_setup running python command "timegrid" 2017-02-05 21:12:46,049 DEBUG quick_setup about to run timegrid a_rr.tmp 2017-02-05 21:12:46,055 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:46,055 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/contour 2017-02-05 21:12:46,055 DEBUG quick_setup running python command "as_cont" 2017-02-05 21:12:46,056 DEBUG quick_setup about to run adcpsect as_cont.tmp 2017-02-05 21:12:46,165 DEBUG quick_setup starting in /home/data/RR1702/proc/os75nb 2017-02-05 21:12:46,165 DEBUG quick_setup executing commands from /home/data/RR1702/proc/os75nb/contour 2017-02-05 21:12:46,165 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_rr 2017-02-05 21:12:46,370 DEBUG quick_asect done running getmat with "allbins" 2017-02-05 21:12:46,370 INFO quick_adcp --------------------------------------------- 2017-02-05 21:12:46,370 INFO quick_adcp writing "cruise_info.txt" 2017-02-05 21:12:46,372 INFO root copying NOFIG to /home/adcp/www/figures/os75nb_hcorr_plot.png 2017-02-05 21:12:46,372 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os75nb_hcorr_plot_thumb.png 2017-02-05 21:12:46,372 DEBUG root matfile is contour/contour_uv.mat 2017-02-05 21:12:46,374 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os75nb_cont_uv.mat 2017-02-05 21:12:46,374 DEBUG root matfile is vector/vector_uv.mat 2017-02-05 21:12:46,375 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os75nb_vect_uv.mat 2017-02-05 21:12:46,375 DEBUG root matfile is contour/contour_xy.mat 2017-02-05 21:12:46,375 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os75nb_cont_xy.mat 2017-02-05 21:12:46,375 DEBUG root matfile is vector/vector_xy.mat 2017-02-05 21:12:46,375 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os75nb_vect_xy.mat 2017-02-05 21:12:46,375 DEBUG root about to copy file edit/a_rr.tem to /home/adcp/www/data/os75nb_temp.asc 2017-02-05 21:12:46,376 INFO root copying edit/a_rr.tem to /home/adcp/www/data/os75nb_temp.asc 2017-02-05 21:12:46,878 DEBUG root about to copy netcdf file /home/data/RR1702/proc/os75nb/contour/os75nb.nc to /home/adcp/www/data/os75nb.nc 2017-02-05 21:12:46,884 INFO root copying /home/data/RR1702/proc/os75nb/contour/os75nb.nc to /home/adcp/www/data/os75nb.nc 2017-02-05 21:12:46,884 INFO root nc_compressed: ddstep is 1 2017-02-05 21:12:46,967 INFO root success: made compressed nc file /home/adcp/uhdas_tmp/os75nb_compr.nc 2017-02-05 21:12:47,014 INFO root generating pingstats for os75nb 2017-02-05 21:12:47,015 INFO root Ending quick_adcp.py