2018-01-30 21:57:35,480 DEBUG root about to write control file parameters to --yearbase 2018 --cruisename km1803 --configtype python --sonar os38bb --dbname a_km --datatype uhdas --cfgpath /home/data/km1803/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 16 --xducer_dy 6 ## see config/km1803_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 2018-01-30 21:57:35,480 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d os38bb 2018-01-30 21:57:35,481 DEBUG quick_setup found cruise_info.hcorr (posmv, pmv, 0) 2018-01-30 21:57:35,481 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2018-01-30 21:57:35,482 INFO quick_setup fix file is a_km.gps 2018-01-30 21:57:35,482 INFO quick_setup reflayer: ref_method = refsm 2018-01-30 21:57:35,482 INFO quick_setup reflayer: refuv_source = nav 2018-01-30 21:57:35,482 INFO quick_setup reflayer: refuv_smoothwin = 3 2018-01-30 21:57:35,482 INFO quick_adcp importing numpy version 1.11.0 2018-01-30 21:57:35,490 INFO quick_adcp importing matplotlib version 1.5.1 2018-01-30 21:57:35,660 DEBUG quick_mpl in Q_mpl 2018-01-30 21:57:35,660 INFO quick_adcp ===================================================== 2018-01-30 21:57:35,660 INFO quick_adcp ===================================================== 2018-01-30 21:57:35,660 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d os38bb 2018-01-30 21:57:35,660 INFO quick_adcp cwd is /home/data/km1803/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 2018-01-30 21:57:35,660 DEBUG quick_asect extracting matlab files for os38bb 2018-01-30 21:57:35,663 DEBUG quick_setup data directory: /home/data/km1803/raw/os38 2018-01-30 21:57:35,663 INFO quick_setup found 63 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/km1803/raw/os38/*.raw" 2018-01-30 21:57:35,663 INFO quick_setup presently in scan, writing filelist to /home/data/km1803/proc/os38bb/ping/datafile_list.txt 2018-01-30 21:57:35,664 INFO quick_setup found 63 raw data files 2018-01-30 21:57:35,664 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/km1803/raw/os38/km2018_024_60929.raw ... 2018-01-30 21:57:35,664 DEBUG quick_adcp Tue Jan 30 21:57:35 2018 running quick_adcp.py as follows: --cntfile /home/data/km1803/proc/os38bb/os38bb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_km 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 36 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/km1803/proc/os38bb/config cntfile /home/data/km1803/proc/os38bb/os38bb_qpy.cnt commands None configtype python cruisename km1803 data_def vmadcp.def data_filelist /home/data/km1803/proc/os38bb/ping/datafile_list.txt datadir /home/data/km1803/raw/os38 datafile_glob *.raw datatype uhdas dbname a_km dday_bailout None debug False ens_len 300 expert None filelist ['/home/data/km1803/raw/os38/km2018_024_60929.raw', '/home/data/km1803/raw/os38/km2018_024_64800.raw', '/home/data/km1803/raw/os38/km2018_024_72000.raw', '/home/data/km1803/raw/os38/km2018_024_79200.raw', '/home/data/km1803/raw/os38/km2018_025_00000.raw', '/home/data/km1803/raw/os38/km2018_025_07200.raw', '/home/data/km1803/raw/os38/km2018_025_14400.raw', '/home/data/km1803/raw/os38/km2018_025_21600.raw', '/home/data/km1803/raw/os38/km2018_025_28800.raw', '/home/data/km1803/raw/os38/km2018_025_36000.raw', '/home/data/km1803/raw/os38/km2018_025_43200.raw', '/home/data/km1803/raw/os38/km2018_025_50400.raw', '/home/data/km1803/raw/os38/km2018_025_57600.raw', '/home/data/km1803/raw/os38/km2018_025_64800.raw', '/home/data/km1803/raw/os38/km2018_025_72000.raw', '/home/data/km1803/raw/os38/km2018_025_79200.raw', '/home/data/km1803/raw/os38/km2018_026_00000.raw', '/home/data/km1803/raw/os38/km2018_026_07200.raw', '/home/data/km1803/raw/os38/km2018_026_14400.raw', '/home/data/km1803/raw/os38/km2018_026_21600.raw', '/home/data/km1803/raw/os38/km2018_026_28800.raw', '/home/data/km1803/raw/os38/km2018_026_36000.raw', '/home/data/km1803/raw/os38/km2018_026_43200.raw', '/home/data/km1803/raw/os38/km2018_026_50400.raw', '/home/data/km1803/raw/os38/km2018_026_57600.raw', '/home/data/km1803/raw/os38/km2018_026_64800.raw', '/home/data/km1803/raw/os38/km2018_026_72000.raw', '/home/data/km1803/raw/os38/km2018_026_79200.raw', '/home/data/km1803/raw/os38/km2018_027_00000.raw', '/home/data/km1803/raw/os38/km2018_027_07200.raw', '/home/data/km1803/raw/os38/km2018_027_14400.raw', '/home/data/km1803/raw/os38/km2018_027_21600.raw', '/home/data/km1803/raw/os38/km2018_027_28800.raw', '/home/data/km1803/raw/os38/km2018_027_36000.raw', '/home/data/km1803/raw/os38/km2018_027_43200.raw', '/home/data/km1803/raw/os38/km2018_027_50400.raw', '/home/data/km1803/raw/os38/km2018_027_57600.raw', '/home/data/km1803/raw/os38/km2018_027_64800.raw', '/home/data/km1803/raw/os38/km2018_027_72000.raw', '/home/data/km1803/raw/os38/km2018_027_79200.raw', '/home/data/km1803/raw/os38/km2018_028_00000.raw', '/home/data/km1803/raw/os38/km2018_028_07200.raw', '/home/data/km1803/raw/os38/km2018_028_14400.raw', '/home/data/km1803/raw/os38/km2018_028_21600.raw', '/home/data/km1803/raw/os38/km2018_028_28800.raw', '/home/data/km1803/raw/os38/km2018_028_36000.raw', '/home/data/km1803/raw/os38/km2018_028_43200.raw', '/home/data/km1803/raw/os38/km2018_028_50400.raw', '/home/data/km1803/raw/os38/km2018_028_57600.raw', '/home/data/km1803/raw/os38/km2018_028_64800.raw', '/home/data/km1803/raw/os38/km2018_028_72000.raw', '/home/data/km1803/raw/os38/km2018_028_79200.raw', '/home/data/km1803/raw/os38/km2018_029_00000.raw', '/home/data/km1803/raw/os38/km2018_029_07200.raw', '/home/data/km1803/raw/os38/km2018_029_14400.raw', '/home/data/km1803/raw/os38/km2018_029_21600.raw', '/home/data/km1803/raw/os38/km2018_029_28800.raw', '/home/data/km1803/raw/os38/km2018_029_36000.raw', '/home/data/km1803/raw/os38/km2018_029_43200.raw', '/home/data/km1803/raw/os38/km2018_029_50400.raw', '/home/data/km1803/raw/os38/km2018_029_57600.raw', '/home/data/km1803/raw/os38/km2018_029_64800.raw', '/home/data/km1803/raw/os38/km2018_029_72000.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 36 fixfile a_km.gps fixfilexy a_km.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 procdir /home/data/km1803/proc/os38bb py_gbindirbase /home/data/km1803/gbin ref_method refsm refuv_inputfile a_km.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 os38bb steps2rerun sum_xducer_dx 16 sum_xducer_dy 6 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_km.agt ub_type 1920 uhdas_config yearbase = 2018 uhdas_dir = /home/data/km1803 sonar = os38bb gbin = /home/data/km1803/gbin gbinsonar = /home/data/km1803/gbin/os38 raw = /home/data/km1803/raw rawsonar = /home/data/km1803/raw/os38 rbin = /home/data/km1803/rbin proc = /home/data/km1803/proc procsonar = /home/data/km1803/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 : posmv pos_msg : gps roll_inst : posmv roll_msg : pmv hcorr = ['posmv', 'pmv', 0.0] acc_heading_cutoff = 0.02 update_gbin False uvwref_end None uvwref_start None vardoc False varvals False wtrk_step 7 xducer_dx 16 xducer_dy 6 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 2018-01-30 21:57:35,664 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:35,664 INFO quick_adcp step 1: set up files in "edit" directory 2018-01-30 21:57:35,664 INFO quick_run file exists (edit/clearflags.tmp). not writing 2018-01-30 21:57:35,664 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:35,664 INFO quick_adcp step 2: scan files for time range 2018-01-30 21:57:35,664 DEBUG quick_npy Starting: scanping 2018-01-30 21:57:35,700 DEBUG quick_npy Ending: scanping 2018-01-30 21:57:35,700 DEBUG quick_subs start_end_time 2018/01/25 16:55:35 to 2018/01/25 17:00:41 2018-01-30 21:57:35,700 DEBUG quick_subs dd0: 24.705266 dd1: 24.708808 2018-01-30 21:57:35,700 INFO quick_adcp looking for database with adcpdb/a_km*.blk 2018-01-30 21:57:35,700 INFO quick_adcp database found: listing blocks 2018-01-30 21:57:35,701 DEBUG quick_subs removing a_kmdir.blk 2018-01-30 21:57:35,701 DEBUG quick_subs about to run mkblkdir 2018-01-30 21:57:35,701 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-01-30 21:57:35,701 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-01-30 21:57:35,707 DEBUG quick_subs database passes. 2018-01-30 21:57:35,707 DEBUG quick_subs start_end_time 2018/01/25 17:00:29 to 2018/01/30 21:50:35 2018-01-30 21:57:35,707 DEBUG quick_subs dd0: 24.708669 dd1: 29.910127 2018-01-30 21:57:35,708 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2018-01-30 21:57:35,708 DEBUG quick_adcp origdb_time_range is 2018/01/25 17:00:29 to 2018/01/30 21:50:35 2018-01-30 21:57:35,708 DEBUG quick_adcp (24.708669 to 29.910127) 2018-01-30 21:57:35,708 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:35,708 INFO quick_adcp step 3: generate averaged data... 2018-01-30 21:57:35,708 INFO quick_run file load/ping_editparams.txt exists. not replacing 2018-01-30 21:57:35,708 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:35,708 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/load 2018-01-30 21:57:35,708 DEBUG quick_setup running python command "run_pingavg_npy" 2018-01-30 21:57:35,708 DEBUG quick_npy Starting: pingavg 2018-01-30 21:57:35,709 DEBUG quick_npy xducerxy is [16, 6] 2018-01-30 21:57:35,709 DEBUG quick_npy uvwref is None 2018-01-30 21:57:35,709 DEBUG quick_npy singleping editing parameters: 2018-01-30 21:57:35,709 DEBUG quick_npy bigtarget_mab_window : 11 2018-01-30 21:57:35,709 DEBUG quick_npy rl_endbin : 20 2018-01-30 21:57:35,709 DEBUG quick_npy max_search_depth : 2000 2018-01-30 21:57:35,709 DEBUG quick_npy cor_cutoff : 120 2018-01-30 21:57:35,710 DEBUG quick_npy ampfilt : 40 2018-01-30 21:57:35,710 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2018-01-30 21:57:35,710 DEBUG quick_npy rl_startbin : 2 2018-01-30 21:57:35,710 DEBUG quick_npy ecutoff : 0.800000 2018-01-30 21:57:35,710 DEBUG quick_npy refavg_valcutoff : 1 2018-01-30 21:57:35,710 DEBUG quick_npy weakprof_percent : 30 2018-01-30 21:57:35,710 DEBUG quick_npy bigtarget_ampthresh : 55 2018-01-30 21:57:35,712 INFO pingavg ---------------- 2018-01-30 21:57:35,712 INFO pingavg sonar is os38bb 2018-01-30 21:57:35,712 INFO pingavg Pingavg.run for time range 29.833390 to 29.914080 2018-01-30 21:57:35,712 INFO pingavg transducer offset: xducer_dx = 16.000, xducer_dy = 6.000 2018-01-30 21:57:35,712 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2018-01-30 21:57:35,712 INFO pingavg ---------------- 2018-01-30 21:57:35,720 DEBUG pingavg Chunk 1 of 1, 29.833390 to 29.914080 2018-01-30 21:57:35,720 DEBUG pingavg Nothing written 2018-01-30 21:57:35,721 DEBUG quick_npy wrote 0 averages 2018-01-30 21:57:35,721 DEBUG quick_npy Ending: pingavg 2018-01-30 21:57:35,721 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:35,721 INFO quick_adcp step 4: load averaged data (to database) 2018-01-30 21:57:35,721 DEBUG quick_subs in del_overlapping 2018-01-30 21:57:35,721 DEBUG quick_subs lastblock: 2018-01-30 21:57:35,721 DEBUG quick_subs 5 2018-01-30 21:57:35,721 DEBUG quick_subs lastcmd: 2018-01-30 21:57:35,721 DEBUG quick_subs 5 2018-01-30 21:57:35,721 DEBUG quick_subs delblks: 2018-01-30 21:57:35,721 DEBUG quick_subs [5] 2018-01-30 21:57:35,721 DEBUG quick_subs loadblks: 2018-01-30 21:57:35,721 DEBUG quick_subs [5] 2018-01-30 21:57:35,722 DEBUG quick_subs about to run mkblkdir 2018-01-30 21:57:35,722 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-01-30 21:57:35,722 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-01-30 21:57:35,728 DEBUG quick_subs database passes. 2018-01-30 21:57:35,729 DEBUG quick_subs start_end_time 2018/01/25 17:00:29 to 2018/01/29 20:55:33 2018-01-30 21:57:35,729 DEBUG quick_subs dd0: 24.708669 dd1: 28.871910 2018-01-30 21:57:35,729 DEBUG quick_run [5] 2018-01-30 21:57:35,729 DEBUG quick_run cmdlist 2018-01-30 21:57:35,729 DEBUG quick_run ['./ens_blk005.cmd'] 2018-01-30 21:57:35,730 INFO quick_run loaded time range: 2018/01/29 21:00:33 to 2018/01/30 21:55:35 2018-01-30 21:57:35,730 DEBUG quick_setup load/ldcodas.tmp exists 2018-01-30 21:57:35,730 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:35,730 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/load 2018-01-30 21:57:35,730 DEBUG quick_setup running python command "ldcodas" 2018-01-30 21:57:35,730 DEBUG quick_subs filling "thisload" timerange 2018-01-30 21:57:35,731 DEBUG quick_subs in ldcodas 2018-01-30 21:57:35,731 DEBUG quick_subs cmdlist: 2018-01-30 21:57:35,731 DEBUG quick_subs ['./ens_blk005.cmd'] 2018-01-30 21:57:35,731 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_km DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2018 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk005.cmd 2018-01-30 21:57:35,731 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2018-01-30 21:57:35,757 INFO quick_run 6 block files present 2018-01-30 21:57:35,757 DEBUG quick_subs removing a_kmdir.blk 2018-01-30 21:57:35,757 DEBUG quick_subs about to run mkblkdir 2018-01-30 21:57:35,757 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-01-30 21:57:35,757 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-01-30 21:57:35,764 DEBUG quick_subs database passes. 2018-01-30 21:57:35,764 DEBUG quick_subs start_end_time 2018/01/25 17:00:29 to 2018/01/30 21:55:35 2018-01-30 21:57:35,764 DEBUG quick_subs dd0: 24.708669 dd1: 29.913600 2018-01-30 21:57:35,764 INFO quick_adcp database time range: 2018-01-30 21:57:35,764 INFO quick_adcp 2018/01/25 17:00:29 to 2018/01/30 21:55:35 2018-01-30 21:57:35,764 INFO quick_adcp (24.708669 to 29.913600) 2018-01-30 21:57:35,764 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:35,764 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/adcpdb 2018-01-30 21:57:35,764 DEBUG quick_setup running python command "lst_conf" 2018-01-30 21:57:35,764 DEBUG quick_subs dbname: a_km output: a_km.cnh time_ranges: all 2018-01-30 21:57:35,765 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2018-01-30 21:57:35,771 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:35,771 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2018-01-30 21:57:35,771 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2018-01-30 21:57:35,771 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:35,771 INFO quick_adcp step 6: run setflags? 2018-01-30 21:57:35,771 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:35,771 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/edit 2018-01-30 21:57:35,771 DEBUG quick_setup running python command "write_setflags" 2018-01-30 21:57:35,771 DEBUG quick_subs dbname: ../adcpdb/a_km pg_min: 50 set_range_bit time_ranges: all 2018-01-30 21:57:35,771 DEBUG quick_setup about to run setflags setflags.tmp 2018-01-30 21:57:35,781 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:35,781 INFO quick_adcp step 7: get navigation 2018-01-30 21:57:35,781 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:35,781 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/nav 2018-01-30 21:57:35,782 DEBUG quick_setup running python command "catnav" 2018-01-30 21:57:35,782 INFO quick_subs navigation file nav/a_km.gps created from load/*.gps2 2018-01-30 21:57:35,783 INFO quick_subs navigation file nav/a_km.agt created from load/*.gpst2 2018-01-30 21:57:35,783 DEBUG quick_mpl Starting plot: uvship 2018-01-30 21:57:36,027 DEBUG quick_mpl Ending plot: uvship 2018-01-30 21:57:36,027 INFO quick_run plotted uvship 2018-01-30 21:57:36,027 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:36,027 INFO quick_adcp step 8: list heading 2018-01-30 21:57:36,027 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2018-01-30 21:57:36,027 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:36,027 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/cal/rotate 2018-01-30 21:57:36,027 DEBUG quick_setup running python command "lst_hdg" 2018-01-30 21:57:36,027 DEBUG quick_subs dbname: ../../adcpdb/a_km output: scn.hdg step_size= 1 year_base= 2018 time_ranges: all 2018-01-30 21:57:36,027 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2018-01-30 21:57:36,036 INFO quick_run ... headings extracted 2018-01-30 21:57:36,036 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:36,036 INFO quick_adcp step 9: plot heading correction 2018-01-30 21:57:36,036 DEBUG quick_run hcorr_inst is posmv 2018-01-30 21:57:36,036 DEBUG quick_mpl Starting plot: hcorr 2018-01-30 21:57:36,047 DEBUG quick_mpl found 5.204924 days of data 2018-01-30 21:57:36,047 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2018-01-30 21:57:36,047 DEBUG quick_mpl printing 2 pages 2018-01-30 21:57:36,521 DEBUG quick_mpl Ending plot: hcorr 2018-01-30 21:57:36,521 INFO quick_run plots are in cal/rotate/*png 2018-01-30 21:57:36,521 INFO quick_adcp ------------------------- 2018-01-30 21:57:36,521 INFO quick_adcp ---- running navsteps --- 2018-01-30 21:57:36,521 INFO quick_adcp ------------------------- 2018-01-30 21:57:36,521 INFO quick_adcp step 10: nav steps: run adcpsect 2018-01-30 21:57:36,521 INFO quick_adcp navstep 1 2018-01-30 21:57:36,521 DEBUG quick_setup nav/as_nav.tmp exists 2018-01-30 21:57:36,521 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:36,521 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/nav 2018-01-30 21:57:36,521 DEBUG quick_setup running python command "as_nav" 2018-01-30 21:57:36,521 DEBUG quick_subs dbname: ../adcpdb/a_km output: a_km 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 2018/01/25 17:00:29 to 2018/01/30 21:55:35 /* the whole time range */ 2018-01-30 21:57:36,521 DEBUG quick_setup about to run adcpsect as_nav.tmp 2018-01-30 21:57:36,533 INFO quick_run ... ran adcpsect for navsteps 2018-01-30 21:57:36,533 INFO quick_adcp ------------------------- 2018-01-30 21:57:36,533 INFO quick_adcp step 11: nav steps: run refabs 2018-01-30 21:57:36,534 INFO quick_adcp navstep 2 2018-01-30 21:57:36,534 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:36,534 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/nav 2018-01-30 21:57:36,534 DEBUG quick_setup running python command "refabs" 2018-01-30 21:57:36,534 DEBUG quick_subs fix_file_type: simple reference_file: a_km.nav fix_file: a_km.gps output: a_km.ref year_base= 2018 ensemble_length= 300 gap_tolerance= 10 2018-01-30 21:57:36,534 DEBUG quick_setup about to run refabs refabs.tmp 2018-01-30 21:57:36,545 INFO quick_run ... ran refabs for navsteps 2018-01-30 21:57:36,545 INFO quick_adcp ------------------------- 2018-01-30 21:57:36,545 INFO quick_adcp step 12: nav steps: run smoothr for plots 2018-01-30 21:57:36,545 INFO quick_adcp navstep 3 2018-01-30 21:57:36,545 DEBUG quick_setup nav/smoothr.tmp exists 2018-01-30 21:57:36,545 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:36,545 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/nav 2018-01-30 21:57:36,545 DEBUG quick_setup running python command "smoothr" 2018-01-30 21:57:36,546 DEBUG quick_subs reference_file: a_km.nav refabs_output: a_km.ref output: a_km.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 2018-01-30 21:57:36,546 DEBUG quick_setup about to run smoothr smoothr.tmp 2018-01-30 21:57:36,584 INFO quick_run ... ran smoothr 2018-01-30 21:57:36,584 INFO quick_adcp ------------------------- 2018-01-30 21:57:36,584 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2018-01-30 21:57:36,584 INFO quick_adcp navstep 4 2018-01-30 21:57:36,584 INFO quick_run smoothing method for ship speed: refsm 2018-01-30 21:57:36,584 INFO quick_run smoothing window: 3 2018-01-30 21:57:36,584 INFO quick_run ship speed source: nav 2018-01-30 21:57:36,584 DEBUG quick_npy Starting: refsm 2018-01-30 21:57:36,643 DEBUG quick_npy Ending: refsm 2018-01-30 21:57:36,643 INFO quick_run ... shipspeed smoothing step done 2018-01-30 21:57:36,643 INFO quick_adcp ------------------------- 2018-01-30 21:57:36,643 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2018-01-30 21:57:36,643 INFO quick_adcp navstep 5 2018-01-30 21:57:36,643 DEBUG quick_setup nav/put_txy.tmp exists 2018-01-30 21:57:36,643 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:36,643 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/nav 2018-01-30 21:57:36,643 DEBUG quick_setup running python command "put_txy" 2018-01-30 21:57:36,643 DEBUG quick_subs dbname: ../adcpdb/a_km position_file: a_km.agt year_base= 2018 tolerance= 5 2018-01-30 21:57:36,643 DEBUG quick_setup about to run put_txy put_txy.tmp 2018-01-30 21:57:36,654 INFO quick_run ... ran put_txy 2018-01-30 21:57:36,654 DEBUG quick_setup nav/put_tuv.tmp exists 2018-01-30 21:57:36,654 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:36,654 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/nav 2018-01-30 21:57:36,654 DEBUG quick_setup running python command "put_tuv" 2018-01-30 21:57:36,654 DEBUG quick_subs dbname: ../adcpdb/a_km shipspeed_file: refsm_tuv.asc year_base= 2018 tolerance= 5 2018-01-30 21:57:36,654 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2018-01-30 21:57:36,663 INFO quick_run ... ran put_tuv 2018-01-30 21:57:36,664 DEBUG quick_mpl Starting plot: nav 2018-01-30 21:57:36,867 DEBUG quick_mpl Ending plot: nav 2018-01-30 21:57:36,868 INFO quick_run ... made navigation plot 2018-01-30 21:57:36,868 INFO quick_adcp ------------------------- 2018-01-30 21:57:36,868 INFO quick_adcp step 15: nav steps: make reflayer plots 2018-01-30 21:57:36,868 INFO quick_adcp navstep 6 2018-01-30 21:57:36,868 DEBUG quick_mpl Starting plot: refl 2018-01-30 21:57:36,892 DEBUG quick_mpl found 5.197910 days of data 2018-01-30 21:57:36,892 DEBUG quick_mpl start day is 24.000000 2018-01-30 21:57:36,892 DEBUG quick_mpl figures with 2.000000 days per page 2018-01-30 21:57:36,893 DEBUG quick_mpl printing 3 pages 2018-01-30 21:57:36,893 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2018-01-30 21:57:37,311 DEBUG quick_mpl Ending plot: refl 2018-01-30 21:57:37,311 INFO quick_run ... made reflayer plots 2018-01-30 21:57:37,311 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:37,311 INFO quick_adcp step 10: find profile flags 2018-01-30 21:57:37,311 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:37,311 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/edit 2018-01-30 21:57:37,312 DEBUG quick_setup running python command "run_autoedit_npy" 2018-01-30 21:57:37,312 DEBUG quick_npy Starting: autoedit 2018-01-30 21:57:37,361 DEBUG pingedit wrote 1 bad bins to abadbin_tmp.asc 2018-01-30 21:57:37,363 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2018-01-30 21:57:37,363 DEBUG quick_npy Ending: autoedit 2018-01-30 21:57:37,363 INFO quick_run ... extracted files using automatic editing 2018-01-30 21:57:37,363 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:37,363 INFO quick_adcp step 11: apply editing 2018-01-30 21:57:37,363 DEBUG quick_run starting in: /home/data/km1803/proc/os38bb 2018-01-30 21:57:37,363 DEBUG quick_run executing commands from: edit 2018-01-30 21:57:37,364 DEBUG quick_run about to run dbupdate ../adcpdb/a_km abadprf_tmp.asc 2018-01-30 21:57:37,369 DEBUG quick_run about to run badbin ../adcpdb/a_km abadbin_tmp.asc 2018-01-30 21:57:37,375 DEBUG quick_subs dbname: ../adcpdb/a_km pg_min: 50 set_range_bit time_ranges: all 2018-01-30 21:57:37,375 DEBUG quick_run about to run setflags setflags.tmp 2018-01-30 21:57:37,386 DEBUG quick_run changing directories back to /home/data/km1803/proc/os38bb 2018-01-30 21:57:37,386 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:37,386 INFO quick_adcp step 12: run calibration steps 2018-01-30 21:57:37,386 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2018-01-30 21:57:37,386 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:37,386 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/cal/botmtrk 2018-01-30 21:57:37,386 DEBUG quick_setup running python command "lst_btrk" 2018-01-30 21:57:37,387 DEBUG quick_subs dbname: ../../adcpdb/a_km output: a_km.btm step_size= 1 year_base= 2018 time_ranges: 2018/01/25 17:00:29 to 2018/01/30 21:55:35 /* whole time range */ 2018-01-30 21:57:37,387 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2018-01-30 21:57:37,394 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2018-01-30 21:57:37,394 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:37,394 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/cal/botmtrk 2018-01-30 21:57:37,394 DEBUG quick_setup running python command "refabsbt" 2018-01-30 21:57:37,394 DEBUG quick_subs fix_file_type: simple reference_file: a_km.btm fix_file: ../../nav/a_km.gps output: a_km.ref year_base= 2018 ensemble_length= 300 gap_tolerance= 60 2018-01-30 21:57:37,394 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2018-01-30 21:57:37,400 INFO quick_run ...bottom track info in check cal/botmtrk 2018-01-30 21:57:37,400 DEBUG quick_mpl Starting plot: btcal 2018-01-30 21:57:37,400 DEBUG quick_mpl No data in a_km.btm 2018-01-30 21:57:37,400 DEBUG quick_mpl Returning from Btplot with no output 2018-01-30 21:57:37,400 DEBUG quick_mpl Ending plot: btcal 2018-01-30 21:57:37,400 DEBUG quick_setup nav/as_nav.tmp exists 2018-01-30 21:57:37,401 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:37,401 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/nav 2018-01-30 21:57:37,401 DEBUG quick_setup running python command "as_nav" 2018-01-30 21:57:37,401 DEBUG quick_subs dbname: ../adcpdb/a_km output: a_km 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 2018/01/25 17:00:29 to 2018/01/30 21:55:35 /* the whole time range */ 2018-01-30 21:57:37,401 DEBUG quick_setup about to run adcpsect as_nav.tmp 2018-01-30 21:57:37,413 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2018-01-30 21:57:37,414 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:37,414 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/cal/watertrk 2018-01-30 21:57:37,414 DEBUG quick_setup running python command "timslip" 2018-01-30 21:57:37,414 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_km.gps reference_file: ../../nav/a_km.nav output_file: a_km_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 2018-01-30 21:57:37,414 DEBUG quick_setup about to run timslip timslip.tmp 2018-01-30 21:57:37,422 INFO quick_run ... watertrack info in cal/watertrk 2018-01-30 21:57:37,422 DEBUG quick_mpl Starting plot: wtcal 2018-01-30 21:57:37,423 DEBUG quick_mpl Found 11 calibration points 2018-01-30 21:57:37,975 DEBUG quick_mpl Ending plot: wtcal 2018-01-30 21:57:37,975 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:37,975 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/cal/watertrk 2018-01-30 21:57:37,975 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2018-01-30 21:57:37,975 DEBUG quick_npy Starting: guess_xducerxy 2018-01-30 21:57:38,018 DEBUG quick_npy Ending: guess_xducerxy 2018-01-30 21:57:38,018 INFO quick_run ... check cal/watertrk for estimate 2018-01-30 21:57:38,018 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:38,018 INFO quick_adcp step 13: extract and plot temperature 2018-01-30 21:57:38,018 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:38,018 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/edit 2018-01-30 21:57:38,018 DEBUG quick_setup running python command "lst_temp" 2018-01-30 21:57:38,018 DEBUG quick_subs dbname: ../adcpdb/a_km output: a_km.tem step_size= 1 year_base= 2018 time_ranges: all 2018-01-30 21:57:38,018 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2018-01-30 21:57:38,028 DEBUG quick_mpl Starting plot: temp 2018-01-30 21:57:38,039 DEBUG quick_mpl plotting 1500 points 2018-01-30 21:57:38,190 DEBUG quick_mpl Ending plot: temp 2018-01-30 21:57:38,190 INFO quick_run plotted temperature 2018-01-30 21:57:38,190 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:38,191 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2018-01-30 21:57:38,191 DEBUG quick_setup edit/lst_npings.tmp exists 2018-01-30 21:57:38,191 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:38,191 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/edit 2018-01-30 21:57:38,191 DEBUG quick_setup running python command "lst_npings" 2018-01-30 21:57:38,191 DEBUG quick_subs dbname: ../adcpdb/a_km output: a_km_npings.txt step_size= 1 year_base= 2018 time_ranges: all 2018-01-30 21:57:38,191 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2018-01-30 21:57:38,201 DEBUG quick_mpl Starting plot: npings 2018-01-30 21:57:38,209 DEBUG quick_mpl plotting 1500 points 2018-01-30 21:57:38,297 DEBUG quick_mpl Ending plot: npings 2018-01-30 21:57:38,297 INFO quick_run ... plotted number of pings per ensemble 2018-01-30 21:57:38,297 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:38,297 INFO quick_adcp step 15: extract matlab "allbins" 2018-01-30 21:57:38,297 DEBUG quick_asect step 18: make matlab files for plotting 2018-01-30 21:57:38,297 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:38,297 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/vector 2018-01-30 21:57:38,297 DEBUG quick_setup running python command "timegrid" 2018-01-30 21:57:38,297 DEBUG quick_setup about to run timegrid a_km.tmp 2018-01-30 21:57:38,303 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:38,303 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/vector 2018-01-30 21:57:38,303 DEBUG quick_setup running python command "as_vect" 2018-01-30 21:57:38,303 DEBUG quick_setup about to run adcpsect as_vect.tmp 2018-01-30 21:57:38,324 DEBUG quick_asect done making vector matfiles 2018-01-30 21:57:38,324 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:38,324 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/contour 2018-01-30 21:57:38,324 DEBUG quick_setup running python command "timegrid" 2018-01-30 21:57:38,324 DEBUG quick_setup about to run timegrid a_km.tmp 2018-01-30 21:57:38,330 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:38,330 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/contour 2018-01-30 21:57:38,331 DEBUG quick_setup running python command "as_cont" 2018-01-30 21:57:38,331 DEBUG quick_setup about to run adcpsect as_cont.tmp 2018-01-30 21:57:38,369 DEBUG quick_setup starting in /home/data/km1803/proc/os38bb 2018-01-30 21:57:38,369 DEBUG quick_setup executing commands from /home/data/km1803/proc/os38bb/contour 2018-01-30 21:57:38,369 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_km 2018-01-30 21:57:38,438 DEBUG quick_asect done running getmat with "allbins" 2018-01-30 21:57:38,438 INFO quick_adcp --------------------------------------------- 2018-01-30 21:57:38,438 INFO quick_adcp writing "cruise_info.txt" 2018-01-30 21:57:38,440 INFO root copying NOFIG to /home/adcp/www/figures/os38bb_hcorr_plot.png 2018-01-30 21:57:38,440 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os38bb_hcorr_plot_thumb.png 2018-01-30 21:57:38,440 DEBUG root matfile is contour/contour_uv.mat 2018-01-30 21:57:38,441 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os38bb_cont_uv.mat 2018-01-30 21:57:38,441 DEBUG root matfile is vector/vector_uv.mat 2018-01-30 21:57:38,441 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os38bb_vect_uv.mat 2018-01-30 21:57:38,441 DEBUG root matfile is contour/contour_xy.mat 2018-01-30 21:57:38,441 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os38bb_cont_xy.mat 2018-01-30 21:57:38,441 DEBUG root matfile is vector/vector_xy.mat 2018-01-30 21:57:38,441 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os38bb_vect_xy.mat 2018-01-30 21:57:38,441 DEBUG root about to copy file edit/a_km.tem to /home/adcp/www/data/os38bb_temp.asc 2018-01-30 21:57:38,441 INFO root copying edit/a_km.tem to /home/adcp/www/data/os38bb_temp.asc 2018-01-30 21:57:38,577 DEBUG root about to copy netcdf file /home/data/km1803/proc/os38bb/contour/os38bb.nc to /home/adcp/www/data/os38bb.nc 2018-01-30 21:57:38,580 INFO root copying /home/data/km1803/proc/os38bb/contour/os38bb.nc to /home/adcp/www/data/os38bb.nc 2018-01-30 21:57:38,580 INFO root nc_compressed: ddstep is 1 2018-01-30 21:57:38,624 INFO root success: made compressed nc file /home/adcp/uhdas_tmp/os38bb_compr.nc 2018-01-30 21:57:38,635 INFO root generating pingstats for os38bb 2018-01-30 21:57:38,635 INFO root Ending quick_adcp.py