2014-12-20 08:00:04,171 DEBUG root about to write control file parameters to --yearbase 2014 --cruisename RR1413 --configtype python --sonar os150nb --dbname a_rr --datatype uhdas --cfgpath /home/data/RR1413/proc/os150nb/config --ens_len 120 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea # xducer_dx, xducer_dy not set ## see config/RR1413_proc.py for other settings --skip_avg ## see above --max_search_depth 1000 --ping_headcorr --proc_engine python --refuv_smoothwin 3 --incremental --find_pflags --top_plotbin 1 --auto 2014-12-20 08:00:04,171 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d os150nb 2014-12-20 08:00:04,172 DEBUG quick_setup found cruise_info.hcorr (ashtech, adu, 0) 2014-12-20 08:00:04,173 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2014-12-20 08:00:04,173 INFO quick_setup fix file is a_rr.gps 2014-12-20 08:00:04,173 INFO quick_setup reflayer: ref_method = refsm 2014-12-20 08:00:04,173 INFO quick_setup reflayer: refuv_source = nav 2014-12-20 08:00:04,173 INFO quick_setup reflayer: refuv_smoothwin = 3 2014-12-20 08:00:04,173 INFO quick_adcp importing numpy version 1.8.1 2014-12-20 08:00:04,184 INFO quick_adcp importing matplotlib version 1.3.1 2014-12-20 08:00:04,298 DEBUG quick_mpl in Q_mpl 2014-12-20 08:00:04,298 INFO quick_adcp ===================================================== 2014-12-20 08:00:04,298 INFO quick_adcp ===================================================== 2014-12-20 08:00:04,298 INFO quick_adcp command line was: /home/currents/programs/uhdas/scripts/run_quick.py -d os150nb 2014-12-20 08:00:04,298 INFO quick_adcp cwd is /home/data/RR1413/proc/os150nb 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 2014-12-20 08:00:04,298 DEBUG quick_asect extracting matlab files for os150, nb pings 2014-12-20 08:00:04,340 DEBUG quick_setup data directory: /home/data/RR1413/raw/os150 2014-12-20 08:00:04,341 INFO quick_setup found 259 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/RR1413/raw/os150/*.raw" 2014-12-20 08:00:04,341 DEBUG quick_setup found 259 files from original filelist 2014-12-20 08:00:04,341 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/RR1413/raw/os150/rr2014_331_85363.raw ... 2014-12-20 08:00:04,342 DEBUG quick_adcp Sat Dec 20 08:00:04 2014 running quick_adcp.py as follows: --cntfile /home/data/RR1413/proc/os150nb/os150nb_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] firstdepth 16 gridnum 80 increment 5 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2014 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/RR1413/proc/os150nb/config cntfile /home/data/RR1413/proc/os150nb/os150nb_qpy.cnt commands None configtype python cruisename RR1413 data_def vmadcp.def datadir /home/data/RR1413/raw/os150 datafile_glob *.raw datatype uhdas dbname a_rr dday_bailout None debug False ens_len 120 expert None filelist ['/home/data/RR1413/raw/os150/rr2014_331_85363.raw', '/home/data/RR1413/raw/os150/rr2014_332_00000.raw', '/home/data/RR1413/raw/os150/rr2014_332_07200.raw', '/home/data/RR1413/raw/os150/rr2014_332_14400.raw', '/home/data/RR1413/raw/os150/rr2014_332_21600.raw', '/home/data/RR1413/raw/os150/rr2014_332_28800.raw', '/home/data/RR1413/raw/os150/rr2014_332_36000.raw', 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'/home/data/RR1413/raw/os150/rr2014_353_00000.raw', '/home/data/RR1413/raw/os150/rr2014_353_07200.raw', '/home/data/RR1413/raw/os150/rr2014_353_14400.raw', '/home/data/RR1413/raw/os150/rr2014_353_21600.raw', '/home/data/RR1413/raw/os150/rr2014_353_28800.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 16 fixfile a_rr.gps fixfilexy a_rr.agt frequency 150 hcorr_inst ashtech help False incremental True instname os150 jitter 15 max_BLKprofiles 300 max_search_depth 1000 maxrunsecs None min_filter_fraction 0.5 model os nosave_editcfg 0 numbins 128 pgmin 50 ping_headcorr True pingtype nb printformats png proc_engine python proc_yearbase 2014 py_gbindirbase /home/data/RR1413/gbin ref_method refsm refuv_inputfile a_rr.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 os150nb 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_rr.gps ub_type 1920 uhdas_config yearbase = 2014 uhdas_dir = /home/data/RR1413 sonar = os150nb gbin = /home/data/RR1413/gbin gbinsonar = /home/data/RR1413/gbin/os150 raw = /home/data/RR1413/raw rawsonar = /home/data/RR1413/raw/os150 rbin = /home/data/RR1413/rbin proc = /home/data/RR1413/proc procsonar = /home/data/RR1413/proc/os150nb other attributes: gbin_params = hdg_inst : hydrins hdg_inst_msgs : [('hydrins', 'hdg'), ('ashtech', 'adu'), ('phins3', 'hdg')] hdg_msg : hdg pitch_inst : ashtech pitch_msg : adu pos_inst : gpsnav pos_msg : gps roll_inst : ashtech roll_msg : adu pingavg_params = hbest : ['hydrins', 'hdg'] head_align : -5.4 tr_depth : 5 velscale : {'scale': 1.0} hcorr = ['ashtech', 'adu', 0.0] acc_heading_cutoff = 0.02 update_gbin False vardoc False varvals False wtrk_step 7 xducer_dx 0 xducer_dy 0 yearbase 2014 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 2014-12-20 08:00:04,342 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:04,342 INFO quick_adcp step 1: set up files in "edit" directory 2014-12-20 08:00:04,342 INFO quick_run file exists (edit/clearflags.tmp). not writing 2014-12-20 08:00:04,342 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:04,342 INFO quick_adcp step 2: scan files for time range 2014-12-20 08:00:04,343 DEBUG quick_npy Starting: scanping 2014-12-20 08:00:04,521 DEBUG quick_npy Ending: scanping 2014-12-20 08:00:04,521 DEBUG quick_subs start_end_time 2014/11/28 23:42:45 to 2014/11/28 23:56:57 2014-12-20 08:00:04,521 DEBUG quick_subs dd0: 331.988021 dd1: 331.997882 2014-12-20 08:00:04,522 INFO quick_adcp looking for database with adcpdb/a_rr*.blk 2014-12-20 08:00:04,522 INFO quick_adcp database found: listing blocks 2014-12-20 08:00:04,522 DEBUG quick_subs removing a_rrdir.blk 2014-12-20 08:00:04,522 DEBUG quick_subs about to run mkblkdir 2014-12-20 08:00:04,522 DEBUG quick_subs database still exists; rerunning mkdirblk 2014-12-20 08:00:04,522 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2014-12-20 08:00:04,532 DEBUG quick_subs database passes. 2014-12-20 08:00:04,533 DEBUG quick_subs start_end_time 2014/11/28 23:44:45 to 2014/12/20 07:43:01 2014-12-20 08:00:04,533 DEBUG quick_subs dd0: 331.989410 dd1: 353.321539 2014-12-20 08:00:04,533 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2014-12-20 08:00:04,533 DEBUG quick_adcp origdb_time_range is 2014/11/28 23:44:45 to 2014/12/20 07:43:01 2014-12-20 08:00:04,533 DEBUG quick_adcp (331.989410 to 353.321539) 2014-12-20 08:00:04,533 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:04,533 INFO quick_adcp step 3: generate averaged data... 2014-12-20 08:00:04,533 INFO quick_run file load/ping_editparams.txt exists. not replacing 2014-12-20 08:00:04,533 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:04,533 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/load 2014-12-20 08:00:04,533 DEBUG quick_setup running python command "run_pingavg_npy" 2014-12-20 08:00:04,533 DEBUG quick_npy Starting: pingavg 2014-12-20 08:00:04,535 DEBUG quick_npy singleping editing parameters: 2014-12-20 08:00:04,535 DEBUG quick_npy bigtarget_mab_window : 11 2014-12-20 08:00:04,535 DEBUG quick_npy rl_endbin : 20 2014-12-20 08:00:04,535 DEBUG quick_npy max_search_depth : 1000 2014-12-20 08:00:04,535 DEBUG quick_npy cor_cutoff : 120 2014-12-20 08:00:04,535 DEBUG quick_npy ampfilt : 40 2014-12-20 08:00:04,535 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2014-12-20 08:00:04,535 DEBUG quick_npy rl_startbin : 2 2014-12-20 08:00:04,535 DEBUG quick_npy ecutoff : 0.800000 2014-12-20 08:00:04,535 DEBUG quick_npy refavg_valcutoff : 1 2014-12-20 08:00:04,535 DEBUG quick_npy weakprof_percent : 30 2014-12-20 08:00:04,535 DEBUG quick_npy bigtarget_ampthresh : 55 2014-12-20 08:00:04,535 DEBUG quick_npy xducerxy is [0, 0] 2014-12-20 08:00:04,543 INFO pingavg ---------------- 2014-12-20 08:00:04,543 INFO pingavg Pingavg.run for time range 353.250004 to 353.332762 2014-12-20 08:00:04,543 INFO pingavg transducer offset: xducer_dx = 0.000, xducer_dy = 0.000 2014-12-20 08:00:04,543 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2014-12-20 08:00:04,543 INFO pingavg ---------------- 2014-12-20 08:00:04,556 DEBUG pingavg Chunk 1 of 1, 353.250004 to 353.332762 2014-12-20 08:00:04,556 DEBUG pingavg Nothing written 2014-12-20 08:00:04,556 DEBUG quick_npy wrote 0 averages 2014-12-20 08:00:04,556 DEBUG quick_npy Ending: pingavg 2014-12-20 08:00:04,557 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:04,557 INFO quick_adcp step 4: load averaged data (to database) 2014-12-20 08:00:04,557 DEBUG quick_subs in del_overlapping 2014-12-20 08:00:04,557 DEBUG quick_subs lastblock: 2014-12-20 08:00:04,557 DEBUG quick_subs 52 2014-12-20 08:00:04,557 DEBUG quick_subs lastcmd: 2014-12-20 08:00:04,557 DEBUG quick_subs 52 2014-12-20 08:00:04,557 DEBUG quick_subs delblks: 2014-12-20 08:00:04,558 DEBUG quick_subs [52] 2014-12-20 08:00:04,558 DEBUG quick_subs loadblks: 2014-12-20 08:00:04,558 DEBUG quick_subs [52] 2014-12-20 08:00:04,558 DEBUG quick_subs about to run mkblkdir 2014-12-20 08:00:04,558 DEBUG quick_subs database still exists; rerunning mkdirblk 2014-12-20 08:00:04,558 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2014-12-20 08:00:04,568 DEBUG quick_subs database passes. 2014-12-20 08:00:04,568 DEBUG quick_subs start_end_time 2014/11/28 23:44:45 to 2014/12/20 06:43:02 2014-12-20 08:00:04,568 DEBUG quick_subs dd0: 331.989410 dd1: 353.279884 2014-12-20 08:00:04,568 DEBUG quick_run [52] 2014-12-20 08:00:04,569 DEBUG quick_run cmdlist 2014-12-20 08:00:04,569 DEBUG quick_run ['./ens_blk052.cmd'] 2014-12-20 08:00:04,569 INFO quick_run loaded time range: 2014/12/20 06:45:02 to 2014/12/20 07:59:01 2014-12-20 08:00:04,569 DEBUG quick_setup load/ldcodas.tmp exists 2014-12-20 08:00:04,569 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:04,569 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/load 2014-12-20 08:00:04,569 DEBUG quick_setup running python command "ldcodas" 2014-12-20 08:00:04,569 DEBUG quick_subs filling "thisload" timerange 2014-12-20 08:00:04,570 DEBUG quick_subs in ldcodas 2014-12-20 08:00:04,570 DEBUG quick_subs cmdlist: 2014-12-20 08:00:04,570 DEBUG quick_subs ['./ens_blk052.cmd'] 2014-12-20 08:00:04,570 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_rr DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2014 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk052.cmd 2014-12-20 08:00:04,570 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2014-12-20 08:00:04,578 INFO quick_run 53 block files present 2014-12-20 08:00:04,578 DEBUG quick_subs removing a_rrdir.blk 2014-12-20 08:00:04,578 DEBUG quick_subs about to run mkblkdir 2014-12-20 08:00:04,578 DEBUG quick_subs database still exists; rerunning mkdirblk 2014-12-20 08:00:04,579 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2014-12-20 08:00:04,588 DEBUG quick_subs database passes. 2014-12-20 08:00:04,589 DEBUG quick_subs start_end_time 2014/11/28 23:44:45 to 2014/12/20 07:59:01 2014-12-20 08:00:04,589 DEBUG quick_subs dd0: 331.989410 dd1: 353.332650 2014-12-20 08:00:04,589 INFO quick_adcp database time range: 2014-12-20 08:00:04,589 INFO quick_adcp 2014/11/28 23:44:45 to 2014/12/20 07:59:01 2014-12-20 08:00:04,589 INFO quick_adcp (331.989410 to 353.332650) 2014-12-20 08:00:04,589 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:04,589 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/adcpdb 2014-12-20 08:00:04,589 DEBUG quick_setup running python command "lst_conf" 2014-12-20 08:00:04,589 DEBUG quick_subs dbname: a_rr output: a_rr.cnh time_ranges: all 2014-12-20 08:00:04,589 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2014-12-20 08:00:04,636 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:04,636 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2014-12-20 08:00:04,636 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2014-12-20 08:00:04,637 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:04,637 INFO quick_adcp step 6: run setflags? 2014-12-20 08:00:04,637 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:04,637 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/edit 2014-12-20 08:00:04,637 DEBUG quick_setup running python command "write_setflags" 2014-12-20 08:00:04,637 DEBUG quick_subs dbname: ../adcpdb/a_rr pg_min: 50 set_range_bit time_ranges: all 2014-12-20 08:00:04,637 DEBUG quick_setup about to run setflags setflags.tmp 2014-12-20 08:00:04,752 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:04,752 INFO quick_adcp step 7: get navigation 2014-12-20 08:00:04,752 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:04,752 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/nav 2014-12-20 08:00:04,752 DEBUG quick_setup running python command "catnav" 2014-12-20 08:00:04,755 INFO quick_subs navigation file nav/a_rr.gps created from load/*.gps2 2014-12-20 08:00:04,758 INFO quick_subs navigation file nav/a_rr.agt created from load/*.gpst2 2014-12-20 08:00:04,762 DEBUG quick_mpl Starting plot: uvship 2014-12-20 08:00:05,214 DEBUG quick_mpl Ending plot: uvship 2014-12-20 08:00:05,214 INFO quick_run plotted uvship 2014-12-20 08:00:05,215 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:05,215 INFO quick_adcp step 8: list heading 2014-12-20 08:00:05,215 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2014-12-20 08:00:05,215 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:05,215 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/cal/rotate 2014-12-20 08:00:05,215 DEBUG quick_setup running python command "lst_hdg" 2014-12-20 08:00:05,215 DEBUG quick_subs dbname: ../../adcpdb/a_rr output: scn.hdg step_size= 1 year_base= 2014 time_ranges: all 2014-12-20 08:00:05,215 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2014-12-20 08:00:05,284 INFO quick_run ... headings extracted 2014-12-20 08:00:05,284 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:05,284 INFO quick_adcp step 9: plot heading correction 2014-12-20 08:00:05,284 DEBUG quick_run hcorr_inst is ashtech 2014-12-20 08:00:05,284 DEBUG quick_mpl Starting plot: hcorr 2014-12-20 08:00:05,364 DEBUG quick_mpl found 21.343245 days of data 2014-12-20 08:00:05,364 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2014-12-20 08:00:05,364 DEBUG quick_mpl printing 6 pages 2014-12-20 08:00:05,863 DEBUG quick_mpl Ending plot: hcorr 2014-12-20 08:00:05,863 INFO quick_run plots are in cal/rotate/*png 2014-12-20 08:00:05,863 INFO quick_adcp ------------------------- 2014-12-20 08:00:05,864 INFO quick_adcp ---- running navsteps --- 2014-12-20 08:00:05,864 INFO quick_adcp ------------------------- 2014-12-20 08:00:05,864 INFO quick_adcp step 10: nav steps: run adcpsect 2014-12-20 08:00:05,864 INFO quick_adcp navstep 1 2014-12-20 08:00:05,864 DEBUG quick_setup nav/as_nav.tmp exists 2014-12-20 08:00:05,864 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:05,864 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/nav 2014-12-20 08:00:05,864 DEBUG quick_setup running python command "as_nav" 2014-12-20 08:00:05,864 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2014 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 2014/11/28 23:44:45 to 2014/12/20 07:59:01 /* the whole time range */ 2014-12-20 08:00:05,864 DEBUG quick_setup about to run adcpsect as_nav.tmp 2014-12-20 08:00:06,014 INFO quick_run ... ran adcpsect for navsteps 2014-12-20 08:00:06,014 INFO quick_adcp ------------------------- 2014-12-20 08:00:06,014 INFO quick_adcp step 11: nav steps: run refabs 2014-12-20 08:00:06,014 INFO quick_adcp navstep 2 2014-12-20 08:00:06,014 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:06,014 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/nav 2014-12-20 08:00:06,014 DEBUG quick_setup running python command "refabs" 2014-12-20 08:00:06,014 DEBUG quick_subs fix_file_type: simple reference_file: a_rr.nav fix_file: a_rr.gps output: a_rr.ref year_base= 2014 ensemble_length= 120 gap_tolerance= 10 2014-12-20 08:00:06,014 DEBUG quick_setup about to run refabs refabs.tmp 2014-12-20 08:00:06,095 INFO quick_run ... ran refabs for navsteps 2014-12-20 08:00:06,095 INFO quick_adcp ------------------------- 2014-12-20 08:00:06,095 INFO quick_adcp step 12: nav steps: run smoothr for plots 2014-12-20 08:00:06,095 INFO quick_adcp navstep 3 2014-12-20 08:00:06,096 DEBUG quick_setup nav/smoothr.tmp exists 2014-12-20 08:00:06,096 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:06,096 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/nav 2014-12-20 08:00:06,096 DEBUG quick_setup running python command "smoothr" 2014-12-20 08:00:06,096 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= 120 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2014-12-20 08:00:06,096 DEBUG quick_setup about to run smoothr smoothr.tmp 2014-12-20 08:00:06,646 INFO quick_run ... ran smoothr 2014-12-20 08:00:06,646 INFO quick_adcp ------------------------- 2014-12-20 08:00:06,646 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2014-12-20 08:00:06,646 INFO quick_adcp navstep 4 2014-12-20 08:00:06,646 INFO quick_run smoothing method for ship speed: refsm 2014-12-20 08:00:06,646 INFO quick_run smoothing window: 3 2014-12-20 08:00:06,646 INFO quick_run ship speed source: nav 2014-12-20 08:00:06,646 DEBUG quick_npy Starting: refsm 2014-12-20 08:00:07,194 DEBUG quick_npy Ending: refsm 2014-12-20 08:00:07,194 INFO quick_run ... shipspeed smoothing step done 2014-12-20 08:00:07,195 INFO quick_adcp ------------------------- 2014-12-20 08:00:07,195 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2014-12-20 08:00:07,195 INFO quick_adcp navstep 5 2014-12-20 08:00:07,195 DEBUG quick_setup nav/put_txy.tmp exists 2014-12-20 08:00:07,195 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:07,195 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/nav 2014-12-20 08:00:07,195 DEBUG quick_setup running python command "put_txy" 2014-12-20 08:00:07,195 DEBUG quick_subs dbname: ../adcpdb/a_rr position_file: a_rr.gps year_base= 2014 tolerance= 5 2014-12-20 08:00:07,195 DEBUG quick_setup about to run put_txy put_txy.tmp 2014-12-20 08:00:07,288 INFO quick_run ... ran put_txy 2014-12-20 08:00:07,289 DEBUG quick_setup nav/put_tuv.tmp exists 2014-12-20 08:00:07,289 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:07,289 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/nav 2014-12-20 08:00:07,289 DEBUG quick_setup running python command "put_tuv" 2014-12-20 08:00:07,289 DEBUG quick_subs dbname: ../adcpdb/a_rr shipspeed_file: refsm_tuv.asc year_base= 2014 tolerance= 5 2014-12-20 08:00:07,289 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2014-12-20 08:00:07,375 INFO quick_run ... ran put_tuv 2014-12-20 08:00:07,376 DEBUG quick_mpl Starting plot: nav 2014-12-20 08:00:07,716 DEBUG quick_mpl Ending plot: nav 2014-12-20 08:00:07,716 INFO quick_run ... made navigation plot 2014-12-20 08:00:07,717 INFO quick_adcp ------------------------- 2014-12-20 08:00:07,717 INFO quick_adcp step 15: nav steps: make reflayer plots 2014-12-20 08:00:07,717 INFO quick_adcp navstep 6 2014-12-20 08:00:07,717 DEBUG quick_mpl Starting plot: refl 2014-12-20 08:00:07,941 DEBUG quick_mpl found 21.339080 days of data 2014-12-20 08:00:07,941 DEBUG quick_mpl start day is 331.000000 2014-12-20 08:00:07,941 DEBUG quick_mpl figures with 2.000000 days per page 2014-12-20 08:00:07,941 DEBUG quick_mpl printing 12 pages 2014-12-20 08:00:07,941 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2014-12-20 08:00:08,453 DEBUG quick_mpl Ending plot: refl 2014-12-20 08:00:08,453 INFO quick_run ... made reflayer plots 2014-12-20 08:00:08,453 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:08,454 INFO quick_adcp step 10: find profile flags 2014-12-20 08:00:08,454 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:08,454 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/edit 2014-12-20 08:00:08,454 DEBUG quick_setup running python command "run_autoedit_npy" 2014-12-20 08:00:08,454 DEBUG quick_npy Starting: autoedit 2014-12-20 08:00:08,810 DEBUG pingedit wrote 33 bad bins to abadbin_tmp.asc 2014-12-20 08:00:08,824 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2014-12-20 08:00:08,824 DEBUG quick_npy Ending: autoedit 2014-12-20 08:00:08,824 INFO quick_run ... extracted files using automatic editing 2014-12-20 08:00:08,824 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:08,824 INFO quick_adcp step 11: apply editing 2014-12-20 08:00:08,824 DEBUG quick_run starting in: /home/data/RR1413/proc/os150nb 2014-12-20 08:00:08,824 DEBUG quick_run executing commands from: edit 2014-12-20 08:00:08,825 DEBUG quick_run about to run dbupdate ../adcpdb/a_rr abadprf_tmp.asc 2014-12-20 08:00:08,831 DEBUG quick_run about to run badbin ../adcpdb/a_rr abadbin_tmp.asc 2014-12-20 08:00:08,840 DEBUG quick_subs dbname: ../adcpdb/a_rr pg_min: 50 set_range_bit time_ranges: all 2014-12-20 08:00:08,840 DEBUG quick_run about to run setflags setflags.tmp 2014-12-20 08:00:08,954 DEBUG quick_run changing directories back to /home/data/RR1413/proc/os150nb 2014-12-20 08:00:08,954 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:08,954 INFO quick_adcp step 12: run calibration steps 2014-12-20 08:00:08,954 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2014-12-20 08:00:08,954 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:08,955 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/cal/botmtrk 2014-12-20 08:00:08,955 DEBUG quick_setup running python command "lst_btrk" 2014-12-20 08:00:08,955 DEBUG quick_subs dbname: ../../adcpdb/a_rr output: a_rr.btm step_size= 1 year_base= 2014 time_ranges: 2014/11/28 23:44:45 to 2014/12/20 07:59:01 /* whole time range */ 2014-12-20 08:00:08,955 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2014-12-20 08:00:08,992 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2014-12-20 08:00:08,992 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:08,992 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/cal/botmtrk 2014-12-20 08:00:08,992 DEBUG quick_setup running python command "refabsbt" 2014-12-20 08:00:08,992 DEBUG quick_subs fix_file_type: simple reference_file: a_rr.btm fix_file: ../../nav/a_rr.gps output: a_rr.ref year_base= 2014 ensemble_length= 120 gap_tolerance= 60 2014-12-20 08:00:08,993 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2014-12-20 08:00:09,000 INFO quick_run ...bottom track info in check cal/botmtrk 2014-12-20 08:00:09,000 DEBUG quick_mpl Starting plot: btcal 2014-12-20 08:00:09,341 DEBUG quick_mpl Ending plot: btcal 2014-12-20 08:00:09,341 DEBUG quick_setup nav/as_nav.tmp exists 2014-12-20 08:00:09,341 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:09,341 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/nav 2014-12-20 08:00:09,341 DEBUG quick_setup running python command "as_nav" 2014-12-20 08:00:09,341 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2014 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 2014/11/28 23:44:45 to 2014/12/20 07:59:01 /* the whole time range */ 2014-12-20 08:00:09,342 DEBUG quick_setup about to run adcpsect as_nav.tmp 2014-12-20 08:00:09,489 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2014-12-20 08:00:09,489 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:09,489 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/cal/watertrk 2014-12-20 08:00:09,490 DEBUG quick_setup running python command "timslip" 2014-12-20 08:00:09,490 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= 2014 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 2014-12-20 08:00:09,490 DEBUG quick_setup about to run timslip timslip.tmp 2014-12-20 08:00:09,523 INFO quick_run ... watertrack info in cal/watertrk 2014-12-20 08:00:09,523 DEBUG quick_mpl Starting plot: wtcal 2014-12-20 08:00:09,525 DEBUG quick_mpl Found 84 calibration points 2014-12-20 08:00:10,143 DEBUG quick_mpl Ending plot: wtcal 2014-12-20 08:00:10,143 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:10,143 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/cal/watertrk 2014-12-20 08:00:10,143 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2014-12-20 08:00:10,143 DEBUG quick_npy Starting: guess_xducerxy 2014-12-20 08:00:10,492 DEBUG quick_npy Ending: guess_xducerxy 2014-12-20 08:00:10,492 INFO quick_run ... check cal/watertrk for estimate 2014-12-20 08:00:10,492 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:10,492 INFO quick_adcp step 13: extract and plot temperature 2014-12-20 08:00:10,492 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:10,492 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/edit 2014-12-20 08:00:10,492 DEBUG quick_setup running python command "lst_temp" 2014-12-20 08:00:10,492 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr.tem step_size= 1 year_base= 2014 time_ranges: all 2014-12-20 08:00:10,493 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2014-12-20 08:00:10,582 DEBUG quick_mpl Starting plot: temp 2014-12-20 08:00:10,661 DEBUG quick_mpl plotting 15338 points 2014-12-20 08:00:10,888 DEBUG quick_mpl Ending plot: temp 2014-12-20 08:00:10,888 INFO quick_run plotted temperature 2014-12-20 08:00:10,888 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:10,888 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2014-12-20 08:00:10,888 DEBUG quick_setup edit/lst_npings.tmp exists 2014-12-20 08:00:10,888 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:10,888 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/edit 2014-12-20 08:00:10,888 DEBUG quick_setup running python command "lst_npings" 2014-12-20 08:00:10,888 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr_npings.txt step_size= 1 year_base= 2014 time_ranges: all 2014-12-20 08:00:10,889 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2014-12-20 08:00:10,963 DEBUG quick_mpl Starting plot: npings 2014-12-20 08:00:11,028 DEBUG quick_mpl plotting 15338 points 2014-12-20 08:00:11,174 DEBUG quick_mpl Ending plot: npings 2014-12-20 08:00:11,174 INFO quick_run ... plotted number of pings per ensemble 2014-12-20 08:00:11,174 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:11,174 INFO quick_adcp step 15: extract matlab "allbins" 2014-12-20 08:00:11,174 DEBUG quick_asect step 18: make matlab files for plotting 2014-12-20 08:00:11,174 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:11,174 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/vector 2014-12-20 08:00:11,175 DEBUG quick_setup running python command "timegrid" 2014-12-20 08:00:11,175 DEBUG quick_setup about to run timegrid a_rr.tmp 2014-12-20 08:00:11,181 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:11,181 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/vector 2014-12-20 08:00:11,182 DEBUG quick_setup running python command "as_vect" 2014-12-20 08:00:11,182 DEBUG quick_setup about to run adcpsect as_vect.tmp 2014-12-20 08:00:11,350 DEBUG quick_asect done making vector matfiles 2014-12-20 08:00:11,350 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:11,351 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/contour 2014-12-20 08:00:11,351 DEBUG quick_setup running python command "timegrid" 2014-12-20 08:00:11,351 DEBUG quick_setup about to run timegrid a_rr.tmp 2014-12-20 08:00:11,359 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:11,359 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/contour 2014-12-20 08:00:11,359 DEBUG quick_setup running python command "as_cont" 2014-12-20 08:00:11,359 DEBUG quick_setup about to run adcpsect as_cont.tmp 2014-12-20 08:00:11,594 DEBUG quick_setup starting in /home/data/RR1413/proc/os150nb 2014-12-20 08:00:11,594 DEBUG quick_setup executing commands from /home/data/RR1413/proc/os150nb/contour 2014-12-20 08:00:11,595 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_rr 2014-12-20 08:00:12,826 DEBUG quick_asect done running getmat with "allbins" 2014-12-20 08:00:12,827 INFO quick_adcp --------------------------------------------- 2014-12-20 08:00:12,827 INFO quick_adcp writing "cruise_info.txt" 2014-12-20 08:00:12,880 INFO root copying NOFIG to /home/adcp/www/figures/os150nb_hcorr_plot.png 2014-12-20 08:00:12,880 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os150nb_hcorr_plot_thumb.png 2014-12-20 08:00:12,880 DEBUG root matfile is contour/contour_uv.mat 2014-12-20 08:00:12,883 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os150nb_cont_uv.mat 2014-12-20 08:00:12,883 DEBUG root matfile is vector/vector_uv.mat 2014-12-20 08:00:12,884 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os150nb_vect_uv.mat 2014-12-20 08:00:12,884 DEBUG root matfile is contour/contour_xy.mat 2014-12-20 08:00:12,884 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os150nb_cont_xy.mat 2014-12-20 08:00:12,884 DEBUG root matfile is vector/vector_xy.mat 2014-12-20 08:00:12,884 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os150nb_vect_xy.mat 2014-12-20 08:00:12,884 DEBUG root about to copy file edit/a_rr.tem to /home/adcp/www/data/os150nb_temp.asc 2014-12-20 08:00:12,885 INFO root copying edit/a_rr.tem to /home/adcp/www/data/os150nb_temp.asc 2014-12-20 08:00:12,892 INFO netcdf Using pupynere. 2014-12-20 08:00:13,327 DEBUG root about to copy netcdf file /home/data/RR1413/proc/os150nb/contour/os150nb.nc to /home/adcp/www/data/os150nb.nc 2014-12-20 08:00:13,345 INFO root copying edit/a_rr.tem to /home/adcp/www/data/os150nb.nc 2014-12-20 08:00:13,422 INFO root generating pingstats for os150nb 2014-12-20 08:00:13,422 INFO root Ending quick_adcp.py