2015-11-16 07:10:23,260 DEBUG root about to write control file parameters to --yearbase 2015 --cruisename RR1516 --configtype python --sonar os150nb --dbname a_rr --datatype uhdas --cfgpath /home/data/RR1516/proc/os150nb/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 -1 --xducer_dy 29 ## see config/RR1516_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 2015-11-16 07:10:23,260 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d os150nb 2015-11-16 07:10:23,261 DEBUG quick_setup found cruise_info.hcorr (ashtech, adu, 0) 2015-11-16 07:10:23,261 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2015-11-16 07:10:23,261 INFO quick_setup fix file is a_rr.gps 2015-11-16 07:10:23,262 INFO quick_setup reflayer: ref_method = refsm 2015-11-16 07:10:23,262 INFO quick_setup reflayer: refuv_source = nav 2015-11-16 07:10:23,262 INFO quick_setup reflayer: refuv_smoothwin = 3 2015-11-16 07:10:23,262 INFO quick_adcp importing numpy version 1.8.1 2015-11-16 07:10:23,273 INFO quick_adcp importing matplotlib version 1.3.1 2015-11-16 07:10:23,373 DEBUG quick_mpl in Q_mpl 2015-11-16 07:10:23,373 INFO quick_adcp ===================================================== 2015-11-16 07:10:23,373 INFO quick_adcp ===================================================== 2015-11-16 07:10:23,373 INFO quick_adcp command line was: /home/currents/programs/uhdas/scripts/run_quick.py -d os150nb 2015-11-16 07:10:23,373 INFO quick_adcp cwd is /home/data/RR1516/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 2015-11-16 07:10:23,373 DEBUG quick_asect extracting matlab files for os150, nb pings 2015-11-16 07:10:23,378 DEBUG quick_setup data directory: /home/data/RR1516/raw/os150 2015-11-16 07:10:23,378 INFO quick_setup found 28 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/RR1516/raw/os150/*.raw" 2015-11-16 07:10:23,378 DEBUG quick_setup found 28 files from original filelist 2015-11-16 07:10:23,378 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/RR1516/raw/os150/rr2015_317_03317.raw ... 2015-11-16 07:10:23,379 DEBUG quick_adcp Mon Nov 16 07:10:23 2015 running quick_adcp.py as follows: --cntfile /home/data/RR1516/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 2015 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/RR1516/proc/os150nb/config cntfile /home/data/RR1516/proc/os150nb/os150nb_qpy.cnt commands None configtype python cruisename RR1516 data_def vmadcp.def datadir /home/data/RR1516/raw/os150 datafile_glob *.raw datatype uhdas dbname a_rr dday_bailout None debug False ens_len 120 expert None filelist ['/home/data/RR1516/raw/os150/rr2015_317_03317.raw', '/home/data/RR1516/raw/os150/rr2015_317_07200.raw', '/home/data/RR1516/raw/os150/rr2015_317_14400.raw', '/home/data/RR1516/raw/os150/rr2015_317_21600.raw', '/home/data/RR1516/raw/os150/rr2015_317_28800.raw', '/home/data/RR1516/raw/os150/rr2015_317_36000.raw', '/home/data/RR1516/raw/os150/rr2015_317_43200.raw', '/home/data/RR1516/raw/os150/rr2015_317_50400.raw', '/home/data/RR1516/raw/os150/rr2015_317_57600.raw', '/home/data/RR1516/raw/os150/rr2015_317_64800.raw', '/home/data/RR1516/raw/os150/rr2015_317_72000.raw', '/home/data/RR1516/raw/os150/rr2015_317_79200.raw', '/home/data/RR1516/raw/os150/rr2015_318_00000.raw', '/home/data/RR1516/raw/os150/rr2015_318_07200.raw', '/home/data/RR1516/raw/os150/rr2015_318_14400.raw', '/home/data/RR1516/raw/os150/rr2015_318_21600.raw', '/home/data/RR1516/raw/os150/rr2015_318_28800.raw', '/home/data/RR1516/raw/os150/rr2015_318_36000.raw', '/home/data/RR1516/raw/os150/rr2015_318_43200.raw', '/home/data/RR1516/raw/os150/rr2015_318_50400.raw', '/home/data/RR1516/raw/os150/rr2015_318_57600.raw', '/home/data/RR1516/raw/os150/rr2015_318_64800.raw', '/home/data/RR1516/raw/os150/rr2015_318_72000.raw', '/home/data/RR1516/raw/os150/rr2015_318_79200.raw', '/home/data/RR1516/raw/os150/rr2015_319_00000.raw', '/home/data/RR1516/raw/os150/rr2015_319_07200.raw', '/home/data/RR1516/raw/os150/rr2015_319_14400.raw', '/home/data/RR1516/raw/os150/rr2015_319_21600.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 2015 py_gbindirbase /home/data/RR1516/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 os150nb steps2rerun sum_xducer_dx -1 sum_xducer_dy 29 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 = 2015 uhdas_dir = /home/data/RR1516 sonar = os150nb gbin = /home/data/RR1516/gbin gbinsonar = /home/data/RR1516/gbin/os150 raw = /home/data/RR1516/raw rawsonar = /home/data/RR1516/raw/os150 rbin = /home/data/RR1516/rbin proc = /home/data/RR1516/proc procsonar = /home/data/RR1516/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 -1 xducer_dy 29 yearbase 2015 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 2015-11-16 07:10:23,379 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:23,379 INFO quick_adcp step 1: set up files in "edit" directory 2015-11-16 07:10:23,379 INFO quick_run file exists (edit/clearflags.tmp). not writing 2015-11-16 07:10:23,379 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:23,379 INFO quick_adcp step 2: scan files for time range 2015-11-16 07:10:23,379 DEBUG quick_npy Starting: scanping 2015-11-16 07:10:23,397 DEBUG quick_npy Ending: scanping 2015-11-16 07:10:23,398 DEBUG quick_subs start_end_time 2015/11/14 00:55:18 to 2015/11/14 01:09:31 2015-11-16 07:10:23,398 DEBUG quick_subs dd0: 317.038403 dd1: 317.048275 2015-11-16 07:10:23,398 INFO quick_adcp looking for database with adcpdb/a_rr*.blk 2015-11-16 07:10:23,398 INFO quick_adcp database found: listing blocks 2015-11-16 07:10:23,398 DEBUG quick_subs removing a_rrdir.blk 2015-11-16 07:10:23,398 DEBUG quick_subs about to run mkblkdir 2015-11-16 07:10:23,398 DEBUG quick_subs database still exists; rerunning mkdirblk 2015-11-16 07:10:23,399 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2015-11-16 07:10:23,404 DEBUG quick_subs database passes. 2015-11-16 07:10:23,404 DEBUG quick_subs start_end_time 2015/11/14 00:57:18 to 2015/11/16 06:53:18 2015-11-16 07:10:23,404 DEBUG quick_subs dd0: 317.039792 dd1: 319.287014 2015-11-16 07:10:23,404 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2015-11-16 07:10:23,404 DEBUG quick_adcp origdb_time_range is 2015/11/14 00:57:18 to 2015/11/16 06:53:18 2015-11-16 07:10:23,404 DEBUG quick_adcp (317.039792 to 319.287014) 2015-11-16 07:10:23,404 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:23,404 INFO quick_adcp step 3: generate averaged data... 2015-11-16 07:10:23,404 INFO quick_run file load/ping_editparams.txt exists. not replacing 2015-11-16 07:10:23,405 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:23,405 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/load 2015-11-16 07:10:23,405 DEBUG quick_setup running python command "run_pingavg_npy" 2015-11-16 07:10:23,405 DEBUG quick_npy Starting: pingavg 2015-11-16 07:10:23,406 DEBUG quick_npy singleping editing parameters: 2015-11-16 07:10:23,406 DEBUG quick_npy bigtarget_mab_window : 11 2015-11-16 07:10:23,406 DEBUG quick_npy rl_endbin : 20 2015-11-16 07:10:23,406 DEBUG quick_npy max_search_depth : 1000 2015-11-16 07:10:23,406 DEBUG quick_npy cor_cutoff : 120 2015-11-16 07:10:23,406 DEBUG quick_npy ampfilt : 40 2015-11-16 07:10:23,406 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2015-11-16 07:10:23,406 DEBUG quick_npy rl_startbin : 2 2015-11-16 07:10:23,406 DEBUG quick_npy ecutoff : 0.800000 2015-11-16 07:10:23,406 DEBUG quick_npy refavg_valcutoff : 1 2015-11-16 07:10:23,406 DEBUG quick_npy weakprof_percent : 30 2015-11-16 07:10:23,406 DEBUG quick_npy bigtarget_ampthresh : 55 2015-11-16 07:10:23,406 DEBUG quick_npy xducerxy is [-1, 29] 2015-11-16 07:10:23,409 INFO pingavg ---------------- 2015-11-16 07:10:23,409 INFO pingavg Pingavg.run for time range 319.250000 to 319.298273 2015-11-16 07:10:23,409 INFO pingavg transducer offset: xducer_dx = -1.000, xducer_dy = 29.000 2015-11-16 07:10:23,409 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2015-11-16 07:10:23,409 INFO pingavg ---------------- 2015-11-16 07:10:23,425 DEBUG pingavg Chunk 1 of 1, 319.250000 to 319.298273 2015-11-16 07:10:23,425 DEBUG pingavg Nothing written 2015-11-16 07:10:23,425 DEBUG quick_npy wrote 0 averages 2015-11-16 07:10:23,425 DEBUG quick_npy Ending: pingavg 2015-11-16 07:10:23,425 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:23,425 INFO quick_adcp step 4: load averaged data (to database) 2015-11-16 07:10:23,426 DEBUG quick_subs in del_overlapping 2015-11-16 07:10:23,426 DEBUG quick_subs lastblock: 2015-11-16 07:10:23,426 DEBUG quick_subs 6 2015-11-16 07:10:23,426 DEBUG quick_subs lastcmd: 2015-11-16 07:10:23,426 DEBUG quick_subs 6 2015-11-16 07:10:23,426 DEBUG quick_subs delblks: 2015-11-16 07:10:23,426 DEBUG quick_subs [6] 2015-11-16 07:10:23,426 DEBUG quick_subs loadblks: 2015-11-16 07:10:23,426 DEBUG quick_subs [6] 2015-11-16 07:10:23,426 DEBUG quick_subs about to run mkblkdir 2015-11-16 07:10:23,426 DEBUG quick_subs database still exists; rerunning mkdirblk 2015-11-16 07:10:23,426 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2015-11-16 07:10:23,432 DEBUG quick_subs database passes. 2015-11-16 07:10:23,432 DEBUG quick_subs start_end_time 2015/11/14 00:57:18 to 2015/11/16 02:55:18 2015-11-16 07:10:23,432 DEBUG quick_subs dd0: 317.039792 dd1: 319.121736 2015-11-16 07:10:23,432 DEBUG quick_run [6] 2015-11-16 07:10:23,432 DEBUG quick_run cmdlist 2015-11-16 07:10:23,432 DEBUG quick_run ['./ens_blk006.cmd'] 2015-11-16 07:10:23,433 INFO quick_run loaded time range: 2015/11/16 02:57:18 to 2015/11/16 07:09:18 2015-11-16 07:10:23,433 DEBUG quick_setup load/ldcodas.tmp exists 2015-11-16 07:10:23,433 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:23,433 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/load 2015-11-16 07:10:23,433 DEBUG quick_setup running python command "ldcodas" 2015-11-16 07:10:23,433 DEBUG quick_subs filling "thisload" timerange 2015-11-16 07:10:23,434 DEBUG quick_subs in ldcodas 2015-11-16 07:10:23,434 DEBUG quick_subs cmdlist: 2015-11-16 07:10:23,434 DEBUG quick_subs ['./ens_blk006.cmd'] 2015-11-16 07:10:23,434 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_rr DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2015 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk006.cmd 2015-11-16 07:10:23,434 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2015-11-16 07:10:23,448 INFO quick_run 7 block files present 2015-11-16 07:10:23,449 DEBUG quick_subs removing a_rrdir.blk 2015-11-16 07:10:23,449 DEBUG quick_subs about to run mkblkdir 2015-11-16 07:10:23,449 DEBUG quick_subs database still exists; rerunning mkdirblk 2015-11-16 07:10:23,449 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2015-11-16 07:10:23,455 DEBUG quick_subs database passes. 2015-11-16 07:10:23,456 DEBUG quick_subs start_end_time 2015/11/14 00:57:18 to 2015/11/16 07:09:18 2015-11-16 07:10:23,456 DEBUG quick_subs dd0: 317.039792 dd1: 319.298125 2015-11-16 07:10:23,456 INFO quick_adcp database time range: 2015-11-16 07:10:23,456 INFO quick_adcp 2015/11/14 00:57:18 to 2015/11/16 07:09:18 2015-11-16 07:10:23,456 INFO quick_adcp (317.039792 to 319.298125) 2015-11-16 07:10:23,456 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:23,456 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/adcpdb 2015-11-16 07:10:23,456 DEBUG quick_setup running python command "lst_conf" 2015-11-16 07:10:23,456 DEBUG quick_subs dbname: a_rr output: a_rr.cnh time_ranges: all 2015-11-16 07:10:23,456 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2015-11-16 07:10:23,466 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:23,466 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2015-11-16 07:10:23,466 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2015-11-16 07:10:23,466 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:23,466 INFO quick_adcp step 6: run setflags? 2015-11-16 07:10:23,467 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:23,467 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/edit 2015-11-16 07:10:23,467 DEBUG quick_setup running python command "write_setflags" 2015-11-16 07:10:23,467 DEBUG quick_subs dbname: ../adcpdb/a_rr pg_min: 50 set_range_bit time_ranges: all 2015-11-16 07:10:23,467 DEBUG quick_setup about to run setflags setflags.tmp 2015-11-16 07:10:23,489 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:23,490 INFO quick_adcp step 7: get navigation 2015-11-16 07:10:23,490 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:23,490 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/nav 2015-11-16 07:10:23,490 DEBUG quick_setup running python command "catnav" 2015-11-16 07:10:23,490 INFO quick_subs navigation file nav/a_rr.gps created from load/*.gps2 2015-11-16 07:10:23,491 INFO quick_subs navigation file nav/a_rr.agt created from load/*.gpst2 2015-11-16 07:10:23,492 DEBUG quick_mpl Starting plot: uvship 2015-11-16 07:10:23,727 DEBUG quick_mpl Ending plot: uvship 2015-11-16 07:10:23,727 INFO quick_run plotted uvship 2015-11-16 07:10:23,727 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:23,727 INFO quick_adcp step 8: list heading 2015-11-16 07:10:23,727 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2015-11-16 07:10:23,727 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:23,727 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/cal/rotate 2015-11-16 07:10:23,727 DEBUG quick_setup running python command "lst_hdg" 2015-11-16 07:10:23,727 DEBUG quick_subs dbname: ../../adcpdb/a_rr output: scn.hdg step_size= 1 year_base= 2015 time_ranges: all 2015-11-16 07:10:23,728 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2015-11-16 07:10:23,738 INFO quick_run ... headings extracted 2015-11-16 07:10:23,738 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:23,738 INFO quick_adcp step 9: plot heading correction 2015-11-16 07:10:23,738 DEBUG quick_run hcorr_inst is ashtech 2015-11-16 07:10:23,738 DEBUG quick_mpl Starting plot: hcorr 2015-11-16 07:10:23,747 DEBUG quick_mpl found 2.258331 days of data 2015-11-16 07:10:23,748 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2015-11-16 07:10:23,748 DEBUG quick_mpl printing 1 pages 2015-11-16 07:10:23,963 DEBUG quick_mpl Ending plot: hcorr 2015-11-16 07:10:23,963 INFO quick_run plots are in cal/rotate/*png 2015-11-16 07:10:23,963 INFO quick_adcp ------------------------- 2015-11-16 07:10:23,963 INFO quick_adcp ---- running navsteps --- 2015-11-16 07:10:23,963 INFO quick_adcp ------------------------- 2015-11-16 07:10:23,964 INFO quick_adcp step 10: nav steps: run adcpsect 2015-11-16 07:10:23,964 INFO quick_adcp navstep 1 2015-11-16 07:10:23,964 DEBUG quick_setup nav/as_nav.tmp exists 2015-11-16 07:10:23,964 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:23,964 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/nav 2015-11-16 07:10:23,964 DEBUG quick_setup running python command "as_nav" 2015-11-16 07:10:23,964 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2015 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 2015/11/14 00:57:18 to 2015/11/16 07:09:18 /* the whole time range */ 2015-11-16 07:10:23,964 DEBUG quick_setup about to run adcpsect as_nav.tmp 2015-11-16 07:10:23,982 INFO quick_run ... ran adcpsect for navsteps 2015-11-16 07:10:23,983 INFO quick_adcp ------------------------- 2015-11-16 07:10:23,983 INFO quick_adcp step 11: nav steps: run refabs 2015-11-16 07:10:23,983 INFO quick_adcp navstep 2 2015-11-16 07:10:23,983 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:23,983 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/nav 2015-11-16 07:10:23,983 DEBUG quick_setup running python command "refabs" 2015-11-16 07:10:23,983 DEBUG quick_subs fix_file_type: simple reference_file: a_rr.nav fix_file: a_rr.gps output: a_rr.ref year_base= 2015 ensemble_length= 120 gap_tolerance= 10 2015-11-16 07:10:23,983 DEBUG quick_setup about to run refabs refabs.tmp 2015-11-16 07:10:23,997 INFO quick_run ... ran refabs for navsteps 2015-11-16 07:10:23,997 INFO quick_adcp ------------------------- 2015-11-16 07:10:23,997 INFO quick_adcp step 12: nav steps: run smoothr for plots 2015-11-16 07:10:23,997 INFO quick_adcp navstep 3 2015-11-16 07:10:23,997 DEBUG quick_setup nav/smoothr.tmp exists 2015-11-16 07:10:23,997 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:23,997 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/nav 2015-11-16 07:10:23,997 DEBUG quick_setup running python command "smoothr" 2015-11-16 07:10:23,997 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 2015-11-16 07:10:23,998 DEBUG quick_setup about to run smoothr smoothr.tmp 2015-11-16 07:10:24,062 INFO quick_run ... ran smoothr 2015-11-16 07:10:24,062 INFO quick_adcp ------------------------- 2015-11-16 07:10:24,063 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2015-11-16 07:10:24,063 INFO quick_adcp navstep 4 2015-11-16 07:10:24,063 INFO quick_run smoothing method for ship speed: refsm 2015-11-16 07:10:24,063 INFO quick_run smoothing window: 3 2015-11-16 07:10:24,063 INFO quick_run ship speed source: nav 2015-11-16 07:10:24,063 DEBUG quick_npy Starting: refsm 2015-11-16 07:10:24,119 DEBUG quick_npy Ending: refsm 2015-11-16 07:10:24,119 INFO quick_run ... shipspeed smoothing step done 2015-11-16 07:10:24,119 INFO quick_adcp ------------------------- 2015-11-16 07:10:24,119 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2015-11-16 07:10:24,119 INFO quick_adcp navstep 5 2015-11-16 07:10:24,119 DEBUG quick_setup nav/put_txy.tmp exists 2015-11-16 07:10:24,119 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:24,119 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/nav 2015-11-16 07:10:24,119 DEBUG quick_setup running python command "put_txy" 2015-11-16 07:10:24,119 DEBUG quick_subs dbname: ../adcpdb/a_rr position_file: a_rr.agt year_base= 2015 tolerance= 5 2015-11-16 07:10:24,119 DEBUG quick_setup about to run put_txy put_txy.tmp 2015-11-16 07:10:24,131 INFO quick_run ... ran put_txy 2015-11-16 07:10:24,131 DEBUG quick_setup nav/put_tuv.tmp exists 2015-11-16 07:10:24,132 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:24,132 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/nav 2015-11-16 07:10:24,132 DEBUG quick_setup running python command "put_tuv" 2015-11-16 07:10:24,132 DEBUG quick_subs dbname: ../adcpdb/a_rr shipspeed_file: refsm_tuv.asc year_base= 2015 tolerance= 5 2015-11-16 07:10:24,132 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2015-11-16 07:10:24,148 INFO quick_run ... ran put_tuv 2015-11-16 07:10:24,148 DEBUG quick_mpl Starting plot: nav 2015-11-16 07:10:24,342 DEBUG quick_mpl Ending plot: nav 2015-11-16 07:10:24,342 INFO quick_run ... made navigation plot 2015-11-16 07:10:24,342 INFO quick_adcp ------------------------- 2015-11-16 07:10:24,342 INFO quick_adcp step 15: nav steps: make reflayer plots 2015-11-16 07:10:24,342 INFO quick_adcp navstep 6 2015-11-16 07:10:24,342 DEBUG quick_mpl Starting plot: refl 2015-11-16 07:10:24,364 DEBUG quick_mpl found 2.254161 days of data 2015-11-16 07:10:24,364 DEBUG quick_mpl start day is 317.000000 2015-11-16 07:10:24,364 DEBUG quick_mpl figures with 2.000000 days per page 2015-11-16 07:10:24,364 DEBUG quick_mpl printing 2 pages 2015-11-16 07:10:24,364 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2015-11-16 07:10:24,765 DEBUG quick_mpl Ending plot: refl 2015-11-16 07:10:24,765 INFO quick_run ... made reflayer plots 2015-11-16 07:10:24,765 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:24,765 INFO quick_adcp step 10: find profile flags 2015-11-16 07:10:24,765 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:24,765 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/edit 2015-11-16 07:10:24,765 DEBUG quick_setup running python command "run_autoedit_npy" 2015-11-16 07:10:24,765 DEBUG quick_npy Starting: autoedit 2015-11-16 07:10:24,814 DEBUG pingedit wrote 1 bad bins to abadbin_tmp.asc 2015-11-16 07:10:24,823 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2015-11-16 07:10:24,823 DEBUG quick_npy Ending: autoedit 2015-11-16 07:10:24,823 INFO quick_run ... extracted files using automatic editing 2015-11-16 07:10:24,823 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:24,823 INFO quick_adcp step 11: apply editing 2015-11-16 07:10:24,823 DEBUG quick_run starting in: /home/data/RR1516/proc/os150nb 2015-11-16 07:10:24,823 DEBUG quick_run executing commands from: edit 2015-11-16 07:10:24,824 DEBUG quick_run about to run dbupdate ../adcpdb/a_rr abadprf_tmp.asc 2015-11-16 07:10:24,827 DEBUG quick_run about to run badbin ../adcpdb/a_rr abadbin_tmp.asc 2015-11-16 07:10:24,831 DEBUG quick_subs dbname: ../adcpdb/a_rr pg_min: 50 set_range_bit time_ranges: all 2015-11-16 07:10:24,831 DEBUG quick_run about to run setflags setflags.tmp 2015-11-16 07:10:24,850 DEBUG quick_run changing directories back to /home/data/RR1516/proc/os150nb 2015-11-16 07:10:24,850 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:24,851 INFO quick_adcp step 12: run calibration steps 2015-11-16 07:10:24,851 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2015-11-16 07:10:24,851 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:24,851 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/cal/botmtrk 2015-11-16 07:10:24,851 DEBUG quick_setup running python command "lst_btrk" 2015-11-16 07:10:24,851 DEBUG quick_subs dbname: ../../adcpdb/a_rr output: a_rr.btm step_size= 1 year_base= 2015 time_ranges: 2015/11/14 00:57:18 to 2015/11/16 07:09:18 /* whole time range */ 2015-11-16 07:10:24,851 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2015-11-16 07:10:24,860 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2015-11-16 07:10:24,860 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:24,860 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/cal/botmtrk 2015-11-16 07:10:24,860 DEBUG quick_setup running python command "refabsbt" 2015-11-16 07:10:24,860 DEBUG quick_subs fix_file_type: simple reference_file: a_rr.btm fix_file: ../../nav/a_rr.gps output: a_rr.ref year_base= 2015 ensemble_length= 120 gap_tolerance= 60 2015-11-16 07:10:24,861 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2015-11-16 07:10:24,865 INFO quick_run ...bottom track info in check cal/botmtrk 2015-11-16 07:10:24,865 DEBUG quick_mpl Starting plot: btcal 2015-11-16 07:10:24,866 DEBUG quick_mpl No data in a_rr.btm 2015-11-16 07:10:24,866 DEBUG quick_mpl Returning from Btplot with no output 2015-11-16 07:10:24,866 DEBUG quick_mpl Ending plot: btcal 2015-11-16 07:10:24,866 DEBUG quick_setup nav/as_nav.tmp exists 2015-11-16 07:10:24,866 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:24,866 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/nav 2015-11-16 07:10:24,866 DEBUG quick_setup running python command "as_nav" 2015-11-16 07:10:24,866 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2015 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 2015/11/14 00:57:18 to 2015/11/16 07:09:18 /* the whole time range */ 2015-11-16 07:10:24,866 DEBUG quick_setup about to run adcpsect as_nav.tmp 2015-11-16 07:10:24,889 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2015-11-16 07:10:24,889 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:24,889 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/cal/watertrk 2015-11-16 07:10:24,889 DEBUG quick_setup running python command "timslip" 2015-11-16 07:10:24,889 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= 2015 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 2015-11-16 07:10:24,889 DEBUG quick_setup about to run timslip timslip.tmp 2015-11-16 07:10:24,894 INFO quick_run ... watertrack info in cal/watertrk 2015-11-16 07:10:24,895 DEBUG quick_mpl Starting plot: wtcal 2015-11-16 07:10:24,895 DEBUG quick_mpl Found 0 calibration points 2015-11-16 07:10:24,895 DEBUG quick_mpl Only 0 valid points found; quitting 2015-11-16 07:10:24,895 DEBUG quick_mpl Ending plot: wtcal 2015-11-16 07:10:24,896 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:24,896 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/cal/watertrk 2015-11-16 07:10:24,896 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2015-11-16 07:10:24,896 DEBUG quick_npy Starting: guess_xducerxy 2015-11-16 07:10:24,938 DEBUG quick_npy Ending: guess_xducerxy 2015-11-16 07:10:24,938 INFO quick_run ... check cal/watertrk for estimate 2015-11-16 07:10:24,938 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:24,938 INFO quick_adcp step 13: extract and plot temperature 2015-11-16 07:10:24,938 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:24,938 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/edit 2015-11-16 07:10:24,938 DEBUG quick_setup running python command "lst_temp" 2015-11-16 07:10:24,938 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr.tem step_size= 1 year_base= 2015 time_ranges: all 2015-11-16 07:10:24,938 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2015-11-16 07:10:24,950 DEBUG quick_mpl Starting plot: temp 2015-11-16 07:10:24,962 DEBUG quick_mpl plotting 1627 points 2015-11-16 07:10:25,105 DEBUG quick_mpl Ending plot: temp 2015-11-16 07:10:25,105 INFO quick_run plotted temperature 2015-11-16 07:10:25,105 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:25,105 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2015-11-16 07:10:25,105 DEBUG quick_setup edit/lst_npings.tmp exists 2015-11-16 07:10:25,105 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:25,105 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/edit 2015-11-16 07:10:25,105 DEBUG quick_setup running python command "lst_npings" 2015-11-16 07:10:25,105 DEBUG quick_subs dbname: ../adcpdb/a_rr output: a_rr_npings.txt step_size= 1 year_base= 2015 time_ranges: all 2015-11-16 07:10:25,105 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2015-11-16 07:10:25,116 DEBUG quick_mpl Starting plot: npings 2015-11-16 07:10:25,124 DEBUG quick_mpl plotting 1627 points 2015-11-16 07:10:25,225 DEBUG quick_mpl Ending plot: npings 2015-11-16 07:10:25,225 INFO quick_run ... plotted number of pings per ensemble 2015-11-16 07:10:25,226 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:25,226 INFO quick_adcp step 15: extract matlab "allbins" 2015-11-16 07:10:25,226 DEBUG quick_asect step 18: make matlab files for plotting 2015-11-16 07:10:25,226 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:25,226 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/vector 2015-11-16 07:10:25,226 DEBUG quick_setup running python command "timegrid" 2015-11-16 07:10:25,226 DEBUG quick_setup about to run timegrid a_rr.tmp 2015-11-16 07:10:25,230 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:25,230 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/vector 2015-11-16 07:10:25,230 DEBUG quick_setup running python command "as_vect" 2015-11-16 07:10:25,230 DEBUG quick_setup about to run adcpsect as_vect.tmp 2015-11-16 07:10:25,254 DEBUG quick_asect done making vector matfiles 2015-11-16 07:10:25,254 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:25,254 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/contour 2015-11-16 07:10:25,254 DEBUG quick_setup running python command "timegrid" 2015-11-16 07:10:25,254 DEBUG quick_setup about to run timegrid a_rr.tmp 2015-11-16 07:10:25,258 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:25,258 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/contour 2015-11-16 07:10:25,258 DEBUG quick_setup running python command "as_cont" 2015-11-16 07:10:25,259 DEBUG quick_setup about to run adcpsect as_cont.tmp 2015-11-16 07:10:25,292 DEBUG quick_setup starting in /home/data/RR1516/proc/os150nb 2015-11-16 07:10:25,292 DEBUG quick_setup executing commands from /home/data/RR1516/proc/os150nb/contour 2015-11-16 07:10:25,293 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_rr 2015-11-16 07:10:25,355 DEBUG quick_asect done running getmat with "allbins" 2015-11-16 07:10:25,355 INFO quick_adcp --------------------------------------------- 2015-11-16 07:10:25,356 INFO quick_adcp writing "cruise_info.txt" 2015-11-16 07:10:25,357 INFO root copying NOFIG to /home/adcp/www/figures/os150nb_hcorr_plot.png 2015-11-16 07:10:25,357 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os150nb_hcorr_plot_thumb.png 2015-11-16 07:10:25,357 DEBUG root matfile is contour/contour_uv.mat 2015-11-16 07:10:25,357 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os150nb_cont_uv.mat 2015-11-16 07:10:25,357 DEBUG root matfile is vector/vector_uv.mat 2015-11-16 07:10:25,357 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os150nb_vect_uv.mat 2015-11-16 07:10:25,357 DEBUG root matfile is contour/contour_xy.mat 2015-11-16 07:10:25,358 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os150nb_cont_xy.mat 2015-11-16 07:10:25,358 DEBUG root matfile is vector/vector_xy.mat 2015-11-16 07:10:25,358 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os150nb_vect_xy.mat 2015-11-16 07:10:25,358 DEBUG root about to copy file edit/a_rr.tem to /home/adcp/www/data/os150nb_temp.asc 2015-11-16 07:10:25,358 INFO root copying edit/a_rr.tem to /home/adcp/www/data/os150nb_temp.asc 2015-11-16 07:10:25,363 INFO netcdf Using pupynere. 2015-11-16 07:10:25,412 DEBUG root about to copy netcdf file /home/data/RR1516/proc/os150nb/contour/os150nb.nc to /home/adcp/www/data/os150nb.nc 2015-11-16 07:10:25,414 INFO root copying edit/a_rr.tem to /home/adcp/www/data/os150nb.nc 2015-11-16 07:10:25,425 INFO root generating pingstats for os150nb 2015-11-16 07:10:25,425 INFO root Ending quick_adcp.py