2018-05-02 21:49:31,457 DEBUG root about to write control file parameters to --yearbase 2018 --cruisename EX1803 --configtype python --sonar os38bb --dbname a_ex --datatype uhdas --cfgpath /home/data/EX1803/proc/os38bb/config --ens_len 300 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea #offset between transducer and gps, applied in at-sea processing # NOTE : read special instructions to change offsets # diagnostics in cal/watertrk/guess_xducerxy.out # parameters used: --xducer_dx 0 --xducer_dy 0 ## see config/EX1803_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 2018-05-02 21:49:31,457 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d os38bb 2018-05-02 21:49:31,459 DEBUG quick_setup found cruise_info.hcorr (posmv, pmv, 0) 2018-05-02 21:49:31,459 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2018-05-02 21:49:31,460 INFO quick_setup fix file is a_ex.gps 2018-05-02 21:49:31,460 INFO quick_setup reflayer: ref_method = refsm 2018-05-02 21:49:31,460 INFO quick_setup reflayer: refuv_source = nav 2018-05-02 21:49:31,460 INFO quick_setup reflayer: refuv_smoothwin = 3 2018-05-02 21:49:31,460 INFO quick_adcp importing numpy version 1.8.2 2018-05-02 21:49:31,474 INFO quick_adcp importing matplotlib version 1.4.3 2018-05-02 21:49:31,576 DEBUG quick_mpl in Q_mpl 2018-05-02 21:49:31,576 INFO quick_adcp ===================================================== 2018-05-02 21:49:31,576 INFO quick_adcp ===================================================== 2018-05-02 21:49:31,576 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d os38bb 2018-05-02 21:49:31,577 INFO quick_adcp cwd is /home/data/EX1803/proc/os38bb 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 2018-05-02 21:49:31,577 DEBUG quick_asect extracting matlab files for os38bb 2018-05-02 21:49:31,582 DEBUG quick_setup data directory: /home/data/EX1803/raw/os38 2018-05-02 21:49:31,583 INFO quick_setup found 84 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/EX1803/raw/os38/*.raw" 2018-05-02 21:49:31,583 DEBUG quick_setup found 84 files from original filelist 2018-05-02 21:49:31,583 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/EX1803/raw/os38/ex2018_105_38898.raw ... 2018-05-02 21:49:31,583 DEBUG quick_adcp Wed May 2 21:49:31 2018 running quick_adcp.py as follows: --cntfile /home/data/EX1803/proc/os38bb/os38bb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_ex dbpath ../adcpdb deeper_boundaries [100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600] firstdepth 23 gridnum 80 increment 20 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2018 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/EX1803/proc/os38bb/config cntfile /home/data/EX1803/proc/os38bb/os38bb_qpy.cnt commands None configtype python cruisename EX1803 data_def vmadcp.def data_filelist None datadir /home/data/EX1803/raw/os38 datafile_glob *.raw datatype uhdas dbname a_ex dday_bailout None debug False ens_len 300 expert None filelist ['/home/data/EX1803/raw/os38/ex2018_105_38898.raw', '/home/data/EX1803/raw/os38/ex2018_105_43200.raw', '/home/data/EX1803/raw/os38/ex2018_105_50400.raw', '/home/data/EX1803/raw/os38/ex2018_105_57600.raw', '/home/data/EX1803/raw/os38/ex2018_105_64800.raw', '/home/data/EX1803/raw/os38/ex2018_105_72000.raw', '/home/data/EX1803/raw/os38/ex2018_106_39069.raw', '/home/data/EX1803/raw/os38/ex2018_106_43200.raw', '/home/data/EX1803/raw/os38/ex2018_106_50400.raw', '/home/data/EX1803/raw/os38/ex2018_106_57600.raw', '/home/data/EX1803/raw/os38/ex2018_106_64800.raw', '/home/data/EX1803/raw/os38/ex2018_106_72000.raw', '/home/data/EX1803/raw/os38/ex2018_107_38771.raw', '/home/data/EX1803/raw/os38/ex2018_107_43200.raw', '/home/data/EX1803/raw/os38/ex2018_107_50400.raw', '/home/data/EX1803/raw/os38/ex2018_107_57600.raw', '/home/data/EX1803/raw/os38/ex2018_107_64800.raw', '/home/data/EX1803/raw/os38/ex2018_107_72000.raw', '/home/data/EX1803/raw/os38/ex2018_108_45225.raw', '/home/data/EX1803/raw/os38/ex2018_108_50400.raw', '/home/data/EX1803/raw/os38/ex2018_108_57600.raw', '/home/data/EX1803/raw/os38/ex2018_108_64800.raw', '/home/data/EX1803/raw/os38/ex2018_108_72000.raw', '/home/data/EX1803/raw/os38/ex2018_109_38491.raw', '/home/data/EX1803/raw/os38/ex2018_109_43200.raw', '/home/data/EX1803/raw/os38/ex2018_109_50400.raw', '/home/data/EX1803/raw/os38/ex2018_109_57600.raw', '/home/data/EX1803/raw/os38/ex2018_109_64800.raw', '/home/data/EX1803/raw/os38/ex2018_109_72000.raw', '/home/data/EX1803/raw/os38/ex2018_114_39114.raw', '/home/data/EX1803/raw/os38/ex2018_114_43200.raw', '/home/data/EX1803/raw/os38/ex2018_114_50400.raw', '/home/data/EX1803/raw/os38/ex2018_114_57600.raw', '/home/data/EX1803/raw/os38/ex2018_114_64800.raw', '/home/data/EX1803/raw/os38/ex2018_114_72000.raw', '/home/data/EX1803/raw/os38/ex2018_114_73693.raw', '/home/data/EX1803/raw/os38/ex2018_115_38383.raw', '/home/data/EX1803/raw/os38/ex2018_115_43200.raw', '/home/data/EX1803/raw/os38/ex2018_115_50400.raw', '/home/data/EX1803/raw/os38/ex2018_115_57600.raw', '/home/data/EX1803/raw/os38/ex2018_115_64800.raw', '/home/data/EX1803/raw/os38/ex2018_115_72000.raw', '/home/data/EX1803/raw/os38/ex2018_116_38139.raw', '/home/data/EX1803/raw/os38/ex2018_116_43200.raw', '/home/data/EX1803/raw/os38/ex2018_116_50400.raw', '/home/data/EX1803/raw/os38/ex2018_116_57600.raw', '/home/data/EX1803/raw/os38/ex2018_116_64800.raw', '/home/data/EX1803/raw/os38/ex2018_116_72000.raw', '/home/data/EX1803/raw/os38/ex2018_116_79200.raw', '/home/data/EX1803/raw/os38/ex2018_117_00000.raw', '/home/data/EX1803/raw/os38/ex2018_117_39603.raw', '/home/data/EX1803/raw/os38/ex2018_117_43200.raw', '/home/data/EX1803/raw/os38/ex2018_117_50400.raw', '/home/data/EX1803/raw/os38/ex2018_117_57600.raw', '/home/data/EX1803/raw/os38/ex2018_117_64800.raw', '/home/data/EX1803/raw/os38/ex2018_117_72000.raw', '/home/data/EX1803/raw/os38/ex2018_117_79200.raw', '/home/data/EX1803/raw/os38/ex2018_118_00000.raw', '/home/data/EX1803/raw/os38/ex2018_118_38429.raw', '/home/data/EX1803/raw/os38/ex2018_118_43200.raw', '/home/data/EX1803/raw/os38/ex2018_118_50400.raw', '/home/data/EX1803/raw/os38/ex2018_118_57600.raw', '/home/data/EX1803/raw/os38/ex2018_118_64800.raw', '/home/data/EX1803/raw/os38/ex2018_118_72000.raw', '/home/data/EX1803/raw/os38/ex2018_118_79200.raw', '/home/data/EX1803/raw/os38/ex2018_119_39078.raw', '/home/data/EX1803/raw/os38/ex2018_119_43200.raw', '/home/data/EX1803/raw/os38/ex2018_119_50400.raw', '/home/data/EX1803/raw/os38/ex2018_119_57600.raw', '/home/data/EX1803/raw/os38/ex2018_119_64800.raw', '/home/data/EX1803/raw/os38/ex2018_119_72000.raw', '/home/data/EX1803/raw/os38/ex2018_119_79200.raw', '/home/data/EX1803/raw/os38/ex2018_120_38630.raw', '/home/data/EX1803/raw/os38/ex2018_120_43200.raw', '/home/data/EX1803/raw/os38/ex2018_120_50400.raw', '/home/data/EX1803/raw/os38/ex2018_120_57600.raw', '/home/data/EX1803/raw/os38/ex2018_120_64800.raw', '/home/data/EX1803/raw/os38/ex2018_120_72000.raw', '/home/data/EX1803/raw/os38/ex2018_121_38969.raw', '/home/data/EX1803/raw/os38/ex2018_121_43200.raw', '/home/data/EX1803/raw/os38/ex2018_121_50400.raw', '/home/data/EX1803/raw/os38/ex2018_121_57600.raw', '/home/data/EX1803/raw/os38/ex2018_121_64800.raw', '/home/data/EX1803/raw/os38/ex2018_121_72000.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 23 fixfile a_ex.gps fixfilexy a_ex.agt frequency 38 hcorr_inst posmv help False incremental True instname os38 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 bb printformats png proc_engine python proc_yearbase 2018 py_gbindirbase /home/data/EX1803/gbin ref_method refsm refuv_inputfile a_ex.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 os38bb 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_ex.gps ub_type 1920 uhdas_config yearbase = 2018 uhdas_dir = /home/data/EX1803 sonar = os38bb gbin = /home/data/EX1803/gbin gbinsonar = /home/data/EX1803/gbin/os38 raw = /home/data/EX1803/raw rawsonar = /home/data/EX1803/raw/os38 rbin = /home/data/EX1803/rbin proc = /home/data/EX1803/proc procsonar = /home/data/EX1803/proc/os38bb other attributes: gbin_params = hdg_inst : gyro hdg_inst_msgs : [('gyro', 'hdg'), ('posmv', 'pmv')] hdg_msg : hdg pitch_inst : posmv pitch_msg : pmv pos_inst : cnav pos_msg : gps roll_inst : posmv roll_msg : pmv hcorr = ['posmv', 'pmv', 0.0] acc_heading_cutoff = 0.028 update_gbin False vardoc False varvals False wtrk_step 7 xducer_dx 0 xducer_dy 0 yearbase 2018 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 2018-05-02 21:49:31,584 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:31,584 INFO quick_adcp step 1: set up files in "edit" directory 2018-05-02 21:49:31,584 INFO quick_run file exists (edit/clearflags.tmp). not writing 2018-05-02 21:49:31,584 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:31,584 INFO quick_adcp step 2: scan files for time range 2018-05-02 21:49:31,584 DEBUG quick_npy Starting: scanping 2018-05-02 21:49:31,646 DEBUG quick_npy Ending: scanping 2018-05-02 21:49:31,647 DEBUG quick_subs start_end_time 2018/04/16 10:48:41 to 2018/04/16 10:58:50 2018-05-02 21:49:31,647 DEBUG quick_subs dd0: 105.450475 dd1: 105.457523 2018-05-02 21:49:31,647 INFO quick_adcp looking for database with adcpdb/a_ex*.blk 2018-05-02 21:49:31,647 INFO quick_adcp database found: listing blocks 2018-05-02 21:49:31,647 DEBUG quick_subs removing a_exdir.blk 2018-05-02 21:49:31,647 DEBUG quick_subs about to run mkblkdir 2018-05-02 21:49:31,647 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-05-02 21:49:31,647 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-05-02 21:49:31,654 DEBUG quick_subs database passes. 2018-05-02 21:49:31,655 DEBUG quick_subs start_end_time 2018/04/16 10:53:41 to 2018/05/02 21:29:53 2018-05-02 21:49:31,655 DEBUG quick_subs dd0: 105.453947 dd1: 121.895752 2018-05-02 21:49:31,655 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2018-05-02 21:49:31,655 DEBUG quick_adcp origdb_time_range is 2018/04/16 10:53:41 to 2018/05/02 21:29:53 2018-05-02 21:49:31,655 DEBUG quick_adcp (105.453947 to 121.895752) 2018-05-02 21:49:31,655 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:31,655 INFO quick_adcp step 3: generate averaged data... 2018-05-02 21:49:31,655 INFO quick_run file load/ping_editparams.txt exists. not replacing 2018-05-02 21:49:31,655 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:31,655 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/load 2018-05-02 21:49:31,655 DEBUG quick_setup running python command "run_pingavg_npy" 2018-05-02 21:49:31,655 DEBUG quick_npy Starting: pingavg 2018-05-02 21:49:31,656 DEBUG quick_npy xducerxy is [0, 0] 2018-05-02 21:49:31,656 DEBUG quick_npy singleping editing parameters: 2018-05-02 21:49:31,656 DEBUG quick_npy bigtarget_mab_window : 11 2018-05-02 21:49:31,656 DEBUG quick_npy rl_endbin : 20 2018-05-02 21:49:31,657 DEBUG quick_npy max_search_depth : 2000 2018-05-02 21:49:31,657 DEBUG quick_npy cor_cutoff : 120 2018-05-02 21:49:31,657 DEBUG quick_npy ampfilt : 40 2018-05-02 21:49:31,657 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2018-05-02 21:49:31,657 DEBUG quick_npy rl_startbin : 2 2018-05-02 21:49:31,657 DEBUG quick_npy ecutoff : 0.800000 2018-05-02 21:49:31,657 DEBUG quick_npy refavg_valcutoff : 1 2018-05-02 21:49:31,657 DEBUG quick_npy weakprof_percent : 30 2018-05-02 21:49:31,657 DEBUG quick_npy bigtarget_ampthresh : 55 2018-05-02 21:49:31,664 INFO pingavg ---------------- 2018-05-02 21:49:31,664 INFO pingavg sonar is os38bb 2018-05-02 21:49:31,664 INFO pingavg Pingavg.run for time range 121.833638 to 121.906307 2018-05-02 21:49:31,664 INFO pingavg transducer offset: xducer_dx = 0.000, xducer_dy = 0.000 2018-05-02 21:49:31,665 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2018-05-02 21:49:31,665 INFO pingavg ---------------- 2018-05-02 21:49:31,679 DEBUG pingavg Chunk 1 of 1, 121.833638 to 121.906307 2018-05-02 21:49:31,679 DEBUG pingavg Nothing written 2018-05-02 21:49:31,679 DEBUG quick_npy wrote 0 averages 2018-05-02 21:49:31,679 DEBUG quick_npy Ending: pingavg 2018-05-02 21:49:31,679 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:31,679 INFO quick_adcp step 4: load averaged data (to database) 2018-05-02 21:49:31,680 DEBUG quick_subs in del_overlapping 2018-05-02 21:49:31,680 DEBUG quick_subs lastblock: 2018-05-02 21:49:31,680 DEBUG quick_subs 12 2018-05-02 21:49:31,680 DEBUG quick_subs lastcmd: 2018-05-02 21:49:31,680 DEBUG quick_subs 12 2018-05-02 21:49:31,680 DEBUG quick_subs delblks: 2018-05-02 21:49:31,680 DEBUG quick_subs [12] 2018-05-02 21:49:31,680 DEBUG quick_subs loadblks: 2018-05-02 21:49:31,680 DEBUG quick_subs [12] 2018-05-02 21:49:31,680 DEBUG quick_subs about to run mkblkdir 2018-05-02 21:49:31,680 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-05-02 21:49:31,680 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-05-02 21:49:31,686 DEBUG quick_subs database passes. 2018-05-02 21:49:31,687 DEBUG quick_subs start_end_time 2018/04/16 10:53:41 to 2018/05/01 21:59:14 2018-05-02 21:49:31,687 DEBUG quick_subs dd0: 105.453947 dd1: 120.916134 2018-05-02 21:49:31,687 DEBUG quick_run [12] 2018-05-02 21:49:31,687 DEBUG quick_run cmdlist 2018-05-02 21:49:31,687 DEBUG quick_run ['./ens_blk012.cmd'] 2018-05-02 21:49:31,688 INFO quick_run loaded time range: 2018/05/02 10:54:55 to 2018/05/02 21:44:53 2018-05-02 21:49:31,688 DEBUG quick_setup load/ldcodas.tmp exists 2018-05-02 21:49:31,688 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:31,688 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/load 2018-05-02 21:49:31,688 DEBUG quick_setup running python command "ldcodas" 2018-05-02 21:49:31,688 DEBUG quick_subs filling "thisload" timerange 2018-05-02 21:49:31,688 DEBUG quick_subs in ldcodas 2018-05-02 21:49:31,688 DEBUG quick_subs cmdlist: 2018-05-02 21:49:31,688 DEBUG quick_subs ['./ens_blk012.cmd'] 2018-05-02 21:49:31,688 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_ex DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2018 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk012.cmd 2018-05-02 21:49:31,689 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2018-05-02 21:49:31,703 INFO quick_run 13 block files present 2018-05-02 21:49:31,704 DEBUG quick_subs removing a_exdir.blk 2018-05-02 21:49:31,704 DEBUG quick_subs about to run mkblkdir 2018-05-02 21:49:31,704 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-05-02 21:49:31,704 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-05-02 21:49:31,710 DEBUG quick_subs database passes. 2018-05-02 21:49:31,710 DEBUG quick_subs start_end_time 2018/04/16 10:53:41 to 2018/05/02 21:44:53 2018-05-02 21:49:31,710 DEBUG quick_subs dd0: 105.453947 dd1: 121.906169 2018-05-02 21:49:31,711 INFO quick_adcp database time range: 2018-05-02 21:49:31,711 INFO quick_adcp 2018/04/16 10:53:41 to 2018/05/02 21:44:53 2018-05-02 21:49:31,711 INFO quick_adcp (105.453947 to 121.906169) 2018-05-02 21:49:31,711 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:31,711 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/adcpdb 2018-05-02 21:49:31,711 DEBUG quick_setup running python command "lst_conf" 2018-05-02 21:49:31,711 DEBUG quick_subs dbname: a_ex output: a_ex.cnh time_ranges: all 2018-05-02 21:49:31,711 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2018-05-02 21:49:31,719 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:31,720 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2018-05-02 21:49:31,720 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2018-05-02 21:49:31,720 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:31,720 INFO quick_adcp step 6: run setflags? 2018-05-02 21:49:31,720 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:31,720 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/edit 2018-05-02 21:49:31,720 DEBUG quick_setup running python command "write_setflags" 2018-05-02 21:49:31,720 DEBUG quick_subs dbname: ../adcpdb/a_ex pg_min: 50 set_range_bit time_ranges: all 2018-05-02 21:49:31,720 DEBUG quick_setup about to run setflags setflags.tmp 2018-05-02 21:49:31,740 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:31,740 INFO quick_adcp step 7: get navigation 2018-05-02 21:49:31,740 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:31,740 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/nav 2018-05-02 21:49:31,740 DEBUG quick_setup running python command "catnav" 2018-05-02 21:49:31,741 INFO quick_subs navigation file nav/a_ex.gps created from load/*.gps2 2018-05-02 21:49:31,742 INFO quick_subs navigation file nav/a_ex.agt created from load/*.gpst2 2018-05-02 21:49:31,743 DEBUG quick_mpl Starting plot: uvship 2018-05-02 21:49:31,988 DEBUG quick_mpl Ending plot: uvship 2018-05-02 21:49:31,988 INFO quick_run plotted uvship 2018-05-02 21:49:31,988 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:31,988 INFO quick_adcp step 8: list heading 2018-05-02 21:49:31,989 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2018-05-02 21:49:31,989 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:31,989 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/cal/rotate 2018-05-02 21:49:31,989 DEBUG quick_setup running python command "lst_hdg" 2018-05-02 21:49:31,989 DEBUG quick_subs dbname: ../../adcpdb/a_ex output: scn.hdg step_size= 1 year_base= 2018 time_ranges: all 2018-05-02 21:49:31,989 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2018-05-02 21:49:32,001 INFO quick_run ... headings extracted 2018-05-02 21:49:32,001 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:32,001 INFO quick_adcp step 9: plot heading correction 2018-05-02 21:49:32,001 DEBUG quick_run hcorr_inst is posmv 2018-05-02 21:49:32,001 DEBUG quick_mpl Starting plot: hcorr 2018-05-02 21:49:32,011 DEBUG quick_mpl found 16.452226 days of data 2018-05-02 21:49:32,011 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2018-05-02 21:49:32,011 DEBUG quick_mpl printing 5 pages 2018-05-02 21:49:32,446 DEBUG quick_mpl Ending plot: hcorr 2018-05-02 21:49:32,446 INFO quick_run plots are in cal/rotate/*png 2018-05-02 21:49:32,446 INFO quick_adcp ------------------------- 2018-05-02 21:49:32,446 INFO quick_adcp ---- running navsteps --- 2018-05-02 21:49:32,446 INFO quick_adcp ------------------------- 2018-05-02 21:49:32,447 INFO quick_adcp step 10: nav steps: run adcpsect 2018-05-02 21:49:32,447 INFO quick_adcp navstep 1 2018-05-02 21:49:32,447 DEBUG quick_setup nav/as_nav.tmp exists 2018-05-02 21:49:32,447 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:32,447 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/nav 2018-05-02 21:49:32,447 DEBUG quick_setup running python command "as_nav" 2018-05-02 21:49:32,447 DEBUG quick_subs dbname: ../adcpdb/a_ex output: a_ex step_size: 1 ndepth: 20 time_ranges: separate year_base= 2018 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 2018/04/16 10:53:41 to 2018/05/02 21:44:53 /* the whole time range */ 2018-05-02 21:49:32,447 DEBUG quick_setup about to run adcpsect as_nav.tmp 2018-05-02 21:49:32,468 INFO quick_run ... ran adcpsect for navsteps 2018-05-02 21:49:32,468 INFO quick_adcp ------------------------- 2018-05-02 21:49:32,468 INFO quick_adcp step 11: nav steps: run refabs 2018-05-02 21:49:32,468 INFO quick_adcp navstep 2 2018-05-02 21:49:32,468 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:32,468 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/nav 2018-05-02 21:49:32,468 DEBUG quick_setup running python command "refabs" 2018-05-02 21:49:32,468 DEBUG quick_subs fix_file_type: simple reference_file: a_ex.nav fix_file: a_ex.gps output: a_ex.ref year_base= 2018 ensemble_length= 300 gap_tolerance= 10 2018-05-02 21:49:32,469 DEBUG quick_setup about to run refabs refabs.tmp 2018-05-02 21:49:32,484 INFO quick_run ... ran refabs for navsteps 2018-05-02 21:49:32,485 INFO quick_adcp ------------------------- 2018-05-02 21:49:32,485 INFO quick_adcp step 12: nav steps: run smoothr for plots 2018-05-02 21:49:32,485 INFO quick_adcp navstep 3 2018-05-02 21:49:32,485 DEBUG quick_setup nav/smoothr.tmp exists 2018-05-02 21:49:32,485 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:32,485 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/nav 2018-05-02 21:49:32,485 DEBUG quick_setup running python command "smoothr" 2018-05-02 21:49:32,485 DEBUG quick_subs reference_file: a_ex.nav refabs_output: a_ex.ref output: a_ex.sm filter_hwidth= 0.0208 min_filter_fraction= 0.5 max_gap_ratio= 0.05 max_gap_distance= 50 max_gap_time= 30 /* 0.5 minutes */ ensemble_time= 300 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2018-05-02 21:49:32,485 DEBUG quick_setup about to run smoothr smoothr.tmp 2018-05-02 21:49:32,544 INFO quick_run ... ran smoothr 2018-05-02 21:49:32,544 INFO quick_adcp ------------------------- 2018-05-02 21:49:32,545 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2018-05-02 21:49:32,545 INFO quick_adcp navstep 4 2018-05-02 21:49:32,545 INFO quick_run smoothing method for ship speed: refsm 2018-05-02 21:49:32,545 INFO quick_run smoothing window: 3 2018-05-02 21:49:32,545 INFO quick_run ship speed source: nav 2018-05-02 21:49:32,545 DEBUG quick_npy Starting: refsm 2018-05-02 21:49:32,670 DEBUG quick_npy Ending: refsm 2018-05-02 21:49:32,670 INFO quick_run ... shipspeed smoothing step done 2018-05-02 21:49:32,670 INFO quick_adcp ------------------------- 2018-05-02 21:49:32,670 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2018-05-02 21:49:32,670 INFO quick_adcp navstep 5 2018-05-02 21:49:32,671 DEBUG quick_setup nav/put_txy.tmp exists 2018-05-02 21:49:32,671 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:32,671 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/nav 2018-05-02 21:49:32,671 DEBUG quick_setup running python command "put_txy" 2018-05-02 21:49:32,671 DEBUG quick_subs dbname: ../adcpdb/a_ex position_file: a_ex.gps year_base= 2018 tolerance= 5 2018-05-02 21:49:32,671 DEBUG quick_setup about to run put_txy put_txy.tmp 2018-05-02 21:49:32,687 INFO quick_run ... ran put_txy 2018-05-02 21:49:32,687 DEBUG quick_setup nav/put_tuv.tmp exists 2018-05-02 21:49:32,687 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:32,687 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/nav 2018-05-02 21:49:32,687 DEBUG quick_setup running python command "put_tuv" 2018-05-02 21:49:32,687 DEBUG quick_subs dbname: ../adcpdb/a_ex shipspeed_file: refsm_tuv.asc year_base= 2018 tolerance= 5 2018-05-02 21:49:32,688 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2018-05-02 21:49:32,706 INFO quick_run ... ran put_tuv 2018-05-02 21:49:32,706 DEBUG quick_mpl Starting plot: nav 2018-05-02 21:49:32,904 DEBUG quick_mpl Ending plot: nav 2018-05-02 21:49:32,904 INFO quick_run ... made navigation plot 2018-05-02 21:49:32,904 INFO quick_adcp ------------------------- 2018-05-02 21:49:32,904 INFO quick_adcp step 15: nav steps: make reflayer plots 2018-05-02 21:49:32,904 INFO quick_adcp navstep 6 2018-05-02 21:49:32,904 DEBUG quick_mpl Starting plot: refl 2018-05-02 21:49:32,928 DEBUG quick_mpl found 16.445283 days of data 2018-05-02 21:49:32,929 DEBUG quick_mpl start day is 105.000000 2018-05-02 21:49:32,929 DEBUG quick_mpl figures with 2.000000 days per page 2018-05-02 21:49:32,929 DEBUG quick_mpl printing 9 pages 2018-05-02 21:49:32,929 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2018-05-02 21:49:33,316 DEBUG quick_mpl Ending plot: refl 2018-05-02 21:49:33,316 INFO quick_run ... made reflayer plots 2018-05-02 21:49:33,316 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:33,316 INFO quick_adcp step 10: find profile flags 2018-05-02 21:49:33,316 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:33,316 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/edit 2018-05-02 21:49:33,316 DEBUG quick_setup running python command "run_autoedit_npy" 2018-05-02 21:49:33,317 DEBUG quick_npy Starting: autoedit 2018-05-02 21:49:33,389 DEBUG pingedit wrote 1 bad bins to abadbin_tmp.asc 2018-05-02 21:49:33,391 ERROR pingedit ===> could not apply jittery mask Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/pycurrents/adcp/pingedit.py", line 768, in get_flags self.cflags.addmask(newmask, 'jittery') File "/usr/local/lib/python2.7/dist-packages/pycurrents/num/nptools.py", line 224, in addmask if mask.itemsize == self.nbytes: AttributeError: 'bool' object has no attribute 'itemsize' 2018-05-02 21:49:33,391 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2018-05-02 21:49:33,391 DEBUG quick_npy Ending: autoedit 2018-05-02 21:49:33,392 INFO quick_run ... extracted files using automatic editing 2018-05-02 21:49:33,392 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:33,392 INFO quick_adcp step 11: apply editing 2018-05-02 21:49:33,392 DEBUG quick_run starting in: /home/data/EX1803/proc/os38bb 2018-05-02 21:49:33,392 DEBUG quick_run executing commands from: edit 2018-05-02 21:49:33,392 DEBUG quick_run about to run dbupdate ../adcpdb/a_ex abadprf_tmp.asc 2018-05-02 21:49:33,398 DEBUG quick_run about to run badbin ../adcpdb/a_ex abadbin_tmp.asc 2018-05-02 21:49:33,404 DEBUG quick_subs dbname: ../adcpdb/a_ex pg_min: 50 set_range_bit time_ranges: all 2018-05-02 21:49:33,404 DEBUG quick_run about to run setflags setflags.tmp 2018-05-02 21:49:33,432 DEBUG quick_run changing directories back to /home/data/EX1803/proc/os38bb 2018-05-02 21:49:33,432 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:33,432 INFO quick_adcp step 12: run calibration steps 2018-05-02 21:49:33,432 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2018-05-02 21:49:33,432 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:33,432 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/cal/botmtrk 2018-05-02 21:49:33,432 DEBUG quick_setup running python command "lst_btrk" 2018-05-02 21:49:33,432 DEBUG quick_subs dbname: ../../adcpdb/a_ex output: a_ex.btm step_size= 1 year_base= 2018 time_ranges: 2018/04/16 10:53:41 to 2018/05/02 21:44:53 /* whole time range */ 2018-05-02 21:49:33,432 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2018-05-02 21:49:33,442 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2018-05-02 21:49:33,442 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:33,442 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/cal/botmtrk 2018-05-02 21:49:33,442 DEBUG quick_setup running python command "refabsbt" 2018-05-02 21:49:33,442 DEBUG quick_subs fix_file_type: simple reference_file: a_ex.btm fix_file: ../../nav/a_ex.gps output: a_ex.ref year_base= 2018 ensemble_length= 300 gap_tolerance= 60 2018-05-02 21:49:33,442 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2018-05-02 21:49:33,447 INFO quick_run ...bottom track info in check cal/botmtrk 2018-05-02 21:49:33,447 DEBUG quick_mpl Starting plot: btcal 2018-05-02 21:49:33,447 DEBUG quick_mpl No data in a_ex.btm 2018-05-02 21:49:33,447 DEBUG quick_mpl Returning from Btplot with no output 2018-05-02 21:49:33,448 DEBUG quick_mpl Ending plot: btcal 2018-05-02 21:49:33,448 DEBUG quick_setup nav/as_nav.tmp exists 2018-05-02 21:49:33,448 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:33,448 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/nav 2018-05-02 21:49:33,448 DEBUG quick_setup running python command "as_nav" 2018-05-02 21:49:33,448 DEBUG quick_subs dbname: ../adcpdb/a_ex output: a_ex step_size: 1 ndepth: 20 time_ranges: separate year_base= 2018 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 2018/04/16 10:53:41 to 2018/05/02 21:44:53 /* the whole time range */ 2018-05-02 21:49:33,448 DEBUG quick_setup about to run adcpsect as_nav.tmp 2018-05-02 21:49:33,474 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2018-05-02 21:49:33,474 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:33,474 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/cal/watertrk 2018-05-02 21:49:33,474 DEBUG quick_setup running python command "timslip" 2018-05-02 21:49:33,474 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_ex.gps reference_file: ../../nav/a_ex.nav output_file: a_ex_7.cal year_base= 2018 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 2018-05-02 21:49:33,474 DEBUG quick_setup about to run timslip timslip.tmp 2018-05-02 21:49:33,482 INFO quick_run ... watertrack info in cal/watertrk 2018-05-02 21:49:33,482 DEBUG quick_mpl Starting plot: wtcal 2018-05-02 21:49:33,483 DEBUG quick_mpl Found 2 calibration points 2018-05-02 21:49:33,993 DEBUG quick_mpl Ending plot: wtcal 2018-05-02 21:49:33,993 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:33,993 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/cal/watertrk 2018-05-02 21:49:33,993 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2018-05-02 21:49:33,993 DEBUG quick_npy Starting: guess_xducerxy 2018-05-02 21:49:34,059 DEBUG quick_npy Ending: guess_xducerxy 2018-05-02 21:49:34,059 INFO quick_run ... check cal/watertrk for estimate 2018-05-02 21:49:34,059 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:34,059 INFO quick_adcp step 13: extract and plot temperature 2018-05-02 21:49:34,059 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:34,059 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/edit 2018-05-02 21:49:34,059 DEBUG quick_setup running python command "lst_temp" 2018-05-02 21:49:34,059 DEBUG quick_subs dbname: ../adcpdb/a_ex output: a_ex.tem step_size= 1 year_base= 2018 time_ranges: all 2018-05-02 21:49:34,059 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2018-05-02 21:49:34,073 DEBUG quick_mpl Starting plot: temp 2018-05-02 21:49:34,088 DEBUG quick_mpl plotting 1803 points 2018-05-02 21:49:34,229 DEBUG quick_mpl Ending plot: temp 2018-05-02 21:49:34,229 INFO quick_run plotted temperature 2018-05-02 21:49:34,229 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:34,229 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2018-05-02 21:49:34,229 DEBUG quick_setup edit/lst_npings.tmp exists 2018-05-02 21:49:34,229 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:34,229 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/edit 2018-05-02 21:49:34,229 DEBUG quick_setup running python command "lst_npings" 2018-05-02 21:49:34,229 DEBUG quick_subs dbname: ../adcpdb/a_ex output: a_ex_npings.txt step_size= 1 year_base= 2018 time_ranges: all 2018-05-02 21:49:34,229 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2018-05-02 21:49:34,243 DEBUG quick_mpl Starting plot: npings 2018-05-02 21:49:34,255 DEBUG quick_mpl plotting 1803 points 2018-05-02 21:49:34,344 DEBUG quick_mpl Ending plot: npings 2018-05-02 21:49:34,344 INFO quick_run ... plotted number of pings per ensemble 2018-05-02 21:49:34,344 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:34,344 INFO quick_adcp step 15: extract matlab "allbins" 2018-05-02 21:49:34,344 DEBUG quick_asect step 18: make matlab files for plotting 2018-05-02 21:49:34,344 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:34,344 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/vector 2018-05-02 21:49:34,344 DEBUG quick_setup running python command "timegrid" 2018-05-02 21:49:34,344 DEBUG quick_setup about to run timegrid a_ex.tmp 2018-05-02 21:49:34,350 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:34,350 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/vector 2018-05-02 21:49:34,350 DEBUG quick_setup running python command "as_vect" 2018-05-02 21:49:34,350 DEBUG quick_setup about to run adcpsect as_vect.tmp 2018-05-02 21:49:34,388 DEBUG quick_asect done making vector matfiles 2018-05-02 21:49:34,388 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:34,388 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/contour 2018-05-02 21:49:34,388 DEBUG quick_setup running python command "timegrid" 2018-05-02 21:49:34,388 DEBUG quick_setup about to run timegrid a_ex.tmp 2018-05-02 21:49:34,394 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:34,394 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/contour 2018-05-02 21:49:34,395 DEBUG quick_setup running python command "as_cont" 2018-05-02 21:49:34,395 DEBUG quick_setup about to run adcpsect as_cont.tmp 2018-05-02 21:49:34,446 DEBUG quick_setup starting in /home/data/EX1803/proc/os38bb 2018-05-02 21:49:34,446 DEBUG quick_setup executing commands from /home/data/EX1803/proc/os38bb/contour 2018-05-02 21:49:34,446 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_ex 2018-05-02 21:49:34,511 DEBUG quick_asect done running getmat with "allbins" 2018-05-02 21:49:34,511 INFO quick_adcp --------------------------------------------- 2018-05-02 21:49:34,511 INFO quick_adcp writing "cruise_info.txt" 2018-05-02 21:49:34,512 INFO root copying NOFIG to /home/adcp/www/figures/os38bb_hcorr_plot.png 2018-05-02 21:49:34,512 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os38bb_hcorr_plot_thumb.png 2018-05-02 21:49:34,512 DEBUG root matfile is contour/contour_uv.mat 2018-05-02 21:49:34,515 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os38bb_cont_uv.mat 2018-05-02 21:49:34,515 DEBUG root matfile is vector/vector_uv.mat 2018-05-02 21:49:34,516 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os38bb_vect_uv.mat 2018-05-02 21:49:34,516 DEBUG root matfile is contour/contour_xy.mat 2018-05-02 21:49:34,516 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os38bb_cont_xy.mat 2018-05-02 21:49:34,516 DEBUG root matfile is vector/vector_xy.mat 2018-05-02 21:49:34,516 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os38bb_vect_xy.mat 2018-05-02 21:49:34,516 DEBUG root about to copy file edit/a_ex.tem to /home/adcp/www/data/os38bb_temp.asc 2018-05-02 21:49:34,516 INFO root copying edit/a_ex.tem to /home/adcp/www/data/os38bb_temp.asc 2018-05-02 21:49:34,859 DEBUG root about to copy netcdf file /home/data/EX1803/proc/os38bb/contour/os38bb.nc to /home/adcp/www/data/os38bb.nc 2018-05-02 21:49:34,862 INFO root copying /home/data/EX1803/proc/os38bb/contour/os38bb.nc to /home/adcp/www/data/os38bb.nc 2018-05-02 21:49:34,862 INFO root nc_compressed: ddstep is 1 2018-05-02 21:49:34,905 INFO root success: made compressed nc file /home/adcp/uhdas_tmp/os38bb_compr.nc 2018-05-02 21:49:34,925 INFO root generating pingstats for os38bb 2018-05-02 21:49:34,925 INFO root Ending quick_adcp.py