2020-03-03 20:46:44,799 DEBUG run_quick about to write control file parameters to --yearbase 2020 --cruisename sh-test-2020-01-02a --configtype python --sonar os75bb --dbname a_sh --datatype uhdas --cfgpath /home/data/sh-test-2020-01-02a/proc/os75bb/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 -2 --xducer_dy 35 ## see config/sh-test-2020-01-02a_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 2020-03-03 20:46:44,800 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d os75bb 2020-03-03 20:46:44,801 DEBUG quick_setup found cruise_info.hcorr (posmv, pmv, 2) 2020-03-03 20:46:44,801 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2020-03-03 20:46:44,801 INFO quick_setup fix file is a_sh.gps 2020-03-03 20:46:44,801 INFO quick_setup reflayer: ref_method = refsm 2020-03-03 20:46:44,801 INFO quick_setup reflayer: refuv_source = nav 2020-03-03 20:46:44,801 INFO quick_setup reflayer: refuv_smoothwin = 3 2020-03-03 20:46:44,802 INFO quick_adcp ===================================================== 2020-03-03 20:46:44,802 INFO quick_adcp ===================================================== 2020-03-03 20:46:44,802 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d os75bb 2020-03-03 20:46:44,802 INFO quick_adcp cwd is /home/data/sh-test-2020-01-02a/proc/os75bb 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 2020-03-03 20:46:44,802 DEBUG quick_asect extracting matlab files for os75bb 2020-03-03 20:46:44,802 DEBUG quick_setup data directory: /home/data/sh-test-2020-01-02a/raw/os75 2020-03-03 20:46:44,803 INFO quick_setup found 2 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/sh-test-2020-01-02a/raw/os75/*.raw" 2020-03-03 20:46:44,803 INFO quick_setup presently in scan, writing filelist to /home/data/sh-test-2020-01-02a/proc/os75bb/ping/datafile_list.txt 2020-03-03 20:46:44,803 INFO quick_setup found 2 raw data files 2020-03-03 20:46:44,803 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/sh-test-2020-01-02a/raw/os75/sh2020_062_72572.raw ... 2020-03-03 20:46:44,803 DEBUG quick_adcp Tue Mar 3 20:46:44 2020 running: /usr/local/currents/bin/run_quick.py -d os75bb ----- adcpsect variables ------ cbasename contour dbname a_sh dbpath ../adcpdb deeper_boundaries [50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775] firstdepth 21 gridnum 80 increment 10 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2020 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/sh-test-2020-01-02a/proc/os75bb/config cntfile /home/data/sh-test-2020-01-02a/proc/os75bb/os75bb_qpy.cnt commands None configtype python cruisename sh-test-2020-01-02a data_def vmadcp.def data_filelist /home/data/sh-test-2020-01-02a/proc/os75bb/ping/datafile_list.txt datadir /home/data/sh-test-2020-01-02a/raw/os75 datafile_glob *.raw datatype uhdas dbname a_sh dday_bailout None debug False ens_len 300 expert None filelist ['/home/data/sh-test-2020-01-02a/raw/os75/sh2020_062_72572.raw', '/home/data/sh-test-2020-01-02a/raw/os75/sh2020_062_72682.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 21 fixfile a_sh.gps fixfilexy a_sh.agt frequency 75 hcorr_inst posmv help False incremental True instname os75 jitter 15 max_BLKprofiles 300 max_search_depth 2000 maxrunsecs None min_filter_fraction 0.5 mixed_pings False model os nosave_editcfg 0 numbins 128 pgmin 50 ping_headcorr True pingpref None pingtype bb printformats png proc_engine python proc_yearbase 2020 procdir /home/data/sh-test-2020-01-02a/proc/os75bb py_gbindirbase /home/data/sh-test-2020-01-02a/gbin ref_method refsm refuv_inputfile a_sh.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 os75bb steps2rerun sum_xducer_dx -2 sum_xducer_dy 35 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_sh.agt ub_type 1920 uhdas_config yearbase = 2020 uhdas_dir = /home/data/sh-test-2020-01-02a sonar = os75bb gbin = /home/data/sh-test-2020-01-02a/gbin gbinsonar = /home/data/sh-test-2020-01-02a/gbin/os75 raw = /home/data/sh-test-2020-01-02a/raw rawsonar = /home/data/sh-test-2020-01-02a/raw/os75 rbin = /home/data/sh-test-2020-01-02a/rbin proc = /home/data/sh-test-2020-01-02a/proc procsonar = /home/data/sh-test-2020-01-02a/proc/os75bb 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 : gpsnav pos_msg : gps roll_inst : posmv roll_msg : pmv hcorr = ['posmv', 'pmv', 2.8] acc_heading_cutoff = 0.02 update_gbin False uvwref_end None uvwref_start None vardoc False varvals False wtrk_step 7 xducer_dx -2 xducer_dy 35 yearbase 2020 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 2020-03-03 20:46:44,803 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:44,803 INFO quick_adcp step 1: set up files in "edit" directory 2020-03-03 20:46:44,803 INFO quick_run file exists (edit/clearflags.tmp). not writing 2020-03-03 20:46:44,803 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:44,803 INFO quick_adcp step 2: scan files for time range 2020-03-03 20:46:44,803 DEBUG quick_npy Starting: scanping 2020-03-03 20:46:44,806 DEBUG quick_npy Ending: scanping 2020-03-03 20:46:44,808 DEBUG quick_subs start_end_time 2020/03/03 20:11:26 to 2020/03/03 20:16:29 2020-03-03 20:46:44,808 DEBUG quick_subs dd0: 62.841273 dd1: 62.844780 2020-03-03 20:46:44,809 DEBUG quick_subs running external command "lstblock adcpdb/a_sh adcpdb/a_sh.lst" 2020-03-03 20:46:44,811 DEBUG quick_subs lstblock ran successfully. 2020-03-03 20:46:44,812 DEBUG quick_subs start_end_time 2020/03/03 20:16:25 to 2020/03/03 20:41:24 2020-03-03 20:46:44,812 DEBUG quick_subs dd0: 62.844734 dd1: 62.862083 2020-03-03 20:46:44,812 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2020-03-03 20:46:44,812 DEBUG quick_adcp origdb_time_range is 2020/03/03 20:16:25 to 2020/03/03 20:41:24 2020-03-03 20:46:44,812 DEBUG quick_adcp (62.844734 to 62.862083) 2020-03-03 20:46:44,812 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:44,812 INFO quick_adcp step 3: generate averaged data... 2020-03-03 20:46:44,812 INFO quick_run file load/ping_editparams.txt exists. not replacing 2020-03-03 20:46:44,812 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:44,812 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/load 2020-03-03 20:46:44,812 DEBUG quick_setup running python command "run_pingavg_npy" 2020-03-03 20:46:44,812 DEBUG quick_npy Starting: pingavg 2020-03-03 20:46:44,813 DEBUG quick_npy xducerxy is [-2, 35] 2020-03-03 20:46:44,813 DEBUG quick_npy uvwref is None 2020-03-03 20:46:44,814 DEBUG quick_npy singleping editing parameters: 2020-03-03 20:46:44,814 DEBUG quick_npy ecutoff : 0.800000 2020-03-03 20:46:44,814 DEBUG quick_npy cor_cutoff : 120 2020-03-03 20:46:44,814 DEBUG quick_npy weakprof_percent : 30 2020-03-03 20:46:44,814 DEBUG quick_npy rl_startbin : 2 2020-03-03 20:46:44,814 DEBUG quick_npy rl_endbin : 20 2020-03-03 20:46:44,814 DEBUG quick_npy refavg_valcutoff : 1 2020-03-03 20:46:44,814 DEBUG quick_npy ampfilt : 40 2020-03-03 20:46:44,814 DEBUG quick_npy max_search_depth : 2000 2020-03-03 20:46:44,814 DEBUG quick_npy bigtarget_ampthresh : 55 2020-03-03 20:46:44,814 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2020-03-03 20:46:44,814 DEBUG quick_npy bigtarget_mab_window : 11 2020-03-03 20:46:44,816 INFO pingavg ---------------- 2020-03-03 20:46:44,816 INFO pingavg sonar is os75bb 2020-03-03 20:46:44,817 INFO pingavg Pingavg.run for time range 62.841277 to 62.865758 2020-03-03 20:46:44,817 INFO pingavg transducer offset: xducer_dx = -2.000, xducer_dy = 35.000 2020-03-03 20:46:44,817 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2020-03-03 20:46:44,817 INFO pingavg ---------------- 2020-03-03 20:46:44,819 DEBUG pingavg Chunk 1 of 1, 62.841277 to 62.865758 2020-03-03 20:46:44,819 DEBUG pingavg Nothing written 2020-03-03 20:46:44,819 DEBUG quick_npy wrote 0 averages 2020-03-03 20:46:44,819 DEBUG quick_npy Ending: pingavg 2020-03-03 20:46:44,819 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:44,820 INFO quick_adcp step 4: load averaged data (to database) 2020-03-03 20:46:44,820 DEBUG quick_subs in del_overlapping: lastblock: 1 lastcmd: 1 delblks: [1] loadblks: [1] 2020-03-03 20:46:44,820 DEBUG quick_run [1] 2020-03-03 20:46:44,820 DEBUG quick_run cmdlist 2020-03-03 20:46:44,820 DEBUG quick_run ['./ens_blk001.cmd'] 2020-03-03 20:46:44,821 DEBUG quick_setup load/ldcodas.tmp exists 2020-03-03 20:46:44,821 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:44,821 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/load 2020-03-03 20:46:44,821 DEBUG quick_setup running python command "ldcodas" 2020-03-03 20:46:44,821 DEBUG quick_subs filling "thisload" timerange 2020-03-03 20:46:44,821 DEBUG quick_subs in ldcodas 2020-03-03 20:46:44,821 DEBUG quick_subs cmdlist: 2020-03-03 20:46:44,821 DEBUG quick_subs ['./ens_blk001.cmd'] 2020-03-03 20:46:44,821 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_sh DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2020 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk001.cmd 2020-03-03 20:46:44,821 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2020-03-03 20:46:44,825 INFO quick_run 2 block files present 2020-03-03 20:46:44,825 DEBUG quick_subs running external command "lstblock adcpdb/a_sh adcpdb/a_sh.lst" 2020-03-03 20:46:44,827 DEBUG quick_subs lstblock ran successfully. 2020-03-03 20:46:44,828 DEBUG quick_subs start_end_time 2020/03/03 20:16:25 to 2020/03/03 20:46:26 2020-03-03 20:46:44,828 DEBUG quick_subs dd0: 62.844734 dd1: 62.865579 2020-03-03 20:46:44,828 INFO quick_adcp database time range: 2020-03-03 20:46:44,828 INFO quick_adcp 2020/03/03 20:16:25 to 2020/03/03 20:46:26 2020-03-03 20:46:44,828 INFO quick_adcp (62.844734 to 62.865579) 2020-03-03 20:46:44,828 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:44,828 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/adcpdb 2020-03-03 20:46:44,828 DEBUG quick_setup running python command "lst_conf" 2020-03-03 20:46:44,828 DEBUG quick_subs dbname: a_sh output: a_sh.cnh time_ranges: all 2020-03-03 20:46:44,829 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2020-03-03 20:46:44,831 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:44,831 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2020-03-03 20:46:44,831 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2020-03-03 20:46:44,831 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:44,831 INFO quick_adcp step 6: run setflags? 2020-03-03 20:46:44,831 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:44,831 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/edit 2020-03-03 20:46:44,832 DEBUG quick_setup running python command "write_setflags" 2020-03-03 20:46:44,832 DEBUG quick_subs dbname: ../adcpdb/a_sh pg_min: 50 set_range_bit time_ranges: all 2020-03-03 20:46:44,832 DEBUG quick_setup about to run setflags setflags.tmp 2020-03-03 20:46:44,834 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:44,834 INFO quick_adcp step 7: get navigation 2020-03-03 20:46:44,835 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:44,835 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/nav 2020-03-03 20:46:44,835 DEBUG quick_setup running python command "catnav" 2020-03-03 20:46:44,835 INFO quick_subs navigation file nav/a_sh.gps created from load/*.gps2 2020-03-03 20:46:44,836 INFO quick_subs navigation file nav/a_sh.agt created from load/*.gpst2 2020-03-03 20:46:44,836 DEBUG quick_mpl Starting plot: uvship 2020-03-03 20:46:45,031 DEBUG quick_mpl Ending plot: uvship 2020-03-03 20:46:45,031 INFO quick_run plotted uvship 2020-03-03 20:46:45,031 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:45,031 INFO quick_adcp step 8: list heading 2020-03-03 20:46:45,031 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2020-03-03 20:46:45,031 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,031 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/cal/rotate 2020-03-03 20:46:45,031 DEBUG quick_setup running python command "lst_hdg" 2020-03-03 20:46:45,031 DEBUG quick_subs dbname: ../../adcpdb/a_sh output: scn.hdg step_size= 1 year_base= 2020 time_ranges: all 2020-03-03 20:46:45,031 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2020-03-03 20:46:45,034 INFO quick_run ... headings extracted 2020-03-03 20:46:45,034 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:45,034 INFO quick_adcp step 9: plot heading correction 2020-03-03 20:46:45,034 DEBUG quick_run hcorr_inst is posmv 2020-03-03 20:46:45,034 DEBUG quick_mpl Starting plot: hcorr 2020-03-03 20:46:45,035 DEBUG quick_mpl found 0.020850 days of data 2020-03-03 20:46:45,035 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2020-03-03 20:46:45,035 DEBUG quick_mpl printing 1 pages 2020-03-03 20:46:45,211 DEBUG quick_mpl Ending plot: hcorr 2020-03-03 20:46:45,211 INFO quick_run plots are in cal/rotate/*png 2020-03-03 20:46:45,212 INFO quick_adcp ------------------------- 2020-03-03 20:46:45,212 INFO quick_adcp ---- running navsteps --- 2020-03-03 20:46:45,212 INFO quick_adcp ------------------------- 2020-03-03 20:46:45,212 INFO quick_adcp step 10: nav steps: run adcpsect 2020-03-03 20:46:45,212 INFO quick_adcp navstep 1 2020-03-03 20:46:45,212 DEBUG quick_setup nav/as_nav.tmp exists 2020-03-03 20:46:45,212 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,212 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/nav 2020-03-03 20:46:45,212 DEBUG quick_setup running python command "as_nav" 2020-03-03 20:46:45,212 DEBUG quick_subs dbname: ../adcpdb/a_sh output: a_sh step_size: 1 ndepth: 20 time_ranges: separate year_base= 2020 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 2020/03/03 20:16:25 to 2020/03/03 20:46:26 /* the whole time range */ 2020-03-03 20:46:45,212 DEBUG quick_setup about to run adcpsect as_nav.tmp 2020-03-03 20:46:45,215 INFO quick_run ... ran adcpsect for navsteps 2020-03-03 20:46:45,216 INFO quick_adcp ------------------------- 2020-03-03 20:46:45,216 INFO quick_adcp step 11: nav steps: run refabs 2020-03-03 20:46:45,216 INFO quick_adcp navstep 2 2020-03-03 20:46:45,216 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,216 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/nav 2020-03-03 20:46:45,216 DEBUG quick_setup running python command "refabs" 2020-03-03 20:46:45,216 DEBUG quick_subs fix_file_type: simple reference_file: a_sh.nav fix_file: a_sh.agt output: a_sh.ref year_base= 2020 ensemble_length= 300 gap_tolerance= 10 2020-03-03 20:46:45,216 DEBUG quick_setup about to run refabs refabs.tmp 2020-03-03 20:46:45,219 INFO quick_run ... ran refabs for navsteps 2020-03-03 20:46:45,219 INFO quick_adcp ------------------------- 2020-03-03 20:46:45,219 INFO quick_adcp step 12: nav steps: run smoothr for plots 2020-03-03 20:46:45,219 INFO quick_adcp navstep 3 2020-03-03 20:46:45,219 DEBUG quick_setup nav/smoothr.tmp exists 2020-03-03 20:46:45,219 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,219 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/nav 2020-03-03 20:46:45,219 DEBUG quick_setup running python command "smoothr" 2020-03-03 20:46:45,219 DEBUG quick_subs reference_file: a_sh.nav refabs_output: a_sh.ref output: a_sh.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 2020-03-03 20:46:45,219 DEBUG quick_setup about to run smoothr smoothr.tmp 2020-03-03 20:46:45,222 INFO quick_run ... ran smoothr 2020-03-03 20:46:45,222 INFO quick_adcp ------------------------- 2020-03-03 20:46:45,222 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2020-03-03 20:46:45,222 INFO quick_adcp navstep 4 2020-03-03 20:46:45,223 INFO quick_run smoothing method for ship speed: refsm 2020-03-03 20:46:45,223 INFO quick_run smoothing window: 3 2020-03-03 20:46:45,223 INFO quick_run ship speed source: nav 2020-03-03 20:46:45,223 DEBUG quick_npy Starting: refsm 2020-03-03 20:46:45,234 DEBUG quick_npy Ending: refsm 2020-03-03 20:46:45,234 INFO quick_run ... shipspeed smoothing step done 2020-03-03 20:46:45,234 INFO quick_adcp ------------------------- 2020-03-03 20:46:45,234 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2020-03-03 20:46:45,234 INFO quick_adcp navstep 5 2020-03-03 20:46:45,234 DEBUG quick_setup nav/put_txy.tmp exists 2020-03-03 20:46:45,234 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,234 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/nav 2020-03-03 20:46:45,234 DEBUG quick_setup running python command "put_txy" 2020-03-03 20:46:45,234 DEBUG quick_subs dbname: ../adcpdb/a_sh position_file: a_sh.agt year_base= 2020 tolerance= 5 2020-03-03 20:46:45,234 DEBUG quick_setup about to run put_txy put_txy.tmp 2020-03-03 20:46:45,237 INFO quick_run ... ran put_txy 2020-03-03 20:46:45,237 DEBUG quick_setup nav/put_tuv.tmp exists 2020-03-03 20:46:45,237 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,238 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/nav 2020-03-03 20:46:45,238 DEBUG quick_setup running python command "put_tuv" 2020-03-03 20:46:45,238 DEBUG quick_subs dbname: ../adcpdb/a_sh shipspeed_file: refsm_tuv.asc year_base= 2020 tolerance= 5 2020-03-03 20:46:45,238 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2020-03-03 20:46:45,240 INFO quick_run ... ran put_tuv 2020-03-03 20:46:45,241 DEBUG quick_mpl Starting plot: nav 2020-03-03 20:46:45,389 DEBUG quick_mpl Ending plot: nav 2020-03-03 20:46:45,389 INFO quick_run ... made navigation plot 2020-03-03 20:46:45,389 INFO quick_adcp ------------------------- 2020-03-03 20:46:45,389 INFO quick_adcp step 15: nav steps: make reflayer plots 2020-03-03 20:46:45,389 INFO quick_adcp navstep 6 2020-03-03 20:46:45,389 DEBUG quick_mpl Starting plot: refl 2020-03-03 20:46:45,390 DEBUG quick_mpl found 0.013899 days of data 2020-03-03 20:46:45,390 DEBUG quick_mpl start day is 62.000000 2020-03-03 20:46:45,390 DEBUG quick_mpl figures with 2.000000 days per page 2020-03-03 20:46:45,390 DEBUG quick_mpl printing 1 pages 2020-03-03 20:46:45,390 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2020-03-03 20:46:45,576 DEBUG quick_mpl Ending plot: refl 2020-03-03 20:46:45,576 INFO quick_run ... made reflayer plots 2020-03-03 20:46:45,576 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:45,576 INFO quick_adcp step 10: find profile flags 2020-03-03 20:46:45,576 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,576 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/edit 2020-03-03 20:46:45,576 DEBUG quick_setup running python command "run_autoedit_npy" 2020-03-03 20:46:45,576 DEBUG quick_npy Starting: autoedit 2020-03-03 20:46:45,589 DEBUG pingedit wrote 1 bad bins to abadbin_tmp.asc 2020-03-03 20:46:45,591 DEBUG pingedit wrote 2 bad profiles to abadprf_tmp.asc 2020-03-03 20:46:45,591 DEBUG quick_npy Ending: autoedit 2020-03-03 20:46:45,591 INFO quick_run ... extracted files using automatic editing 2020-03-03 20:46:45,591 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:45,591 INFO quick_adcp step 11: apply editing 2020-03-03 20:46:45,591 DEBUG quick_run starting in: /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,591 DEBUG quick_run executing commands from: edit 2020-03-03 20:46:45,592 DEBUG quick_run about to run dbupdate ../adcpdb/a_sh abadprf_tmp.asc 2020-03-03 20:46:45,595 DEBUG quick_run about to run badbin ../adcpdb/a_sh abadbin_tmp.asc 2020-03-03 20:46:45,598 DEBUG quick_subs dbname: ../adcpdb/a_sh pg_min: 50 set_range_bit time_ranges: all 2020-03-03 20:46:45,598 DEBUG quick_run about to run setflags setflags.tmp 2020-03-03 20:46:45,601 DEBUG quick_run changing directories back to /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,601 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:45,601 INFO quick_adcp step 12: run calibration steps 2020-03-03 20:46:45,601 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2020-03-03 20:46:45,601 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,601 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/cal/botmtrk 2020-03-03 20:46:45,601 DEBUG quick_setup running python command "lst_btrk" 2020-03-03 20:46:45,601 DEBUG quick_subs dbname: ../../adcpdb/a_sh output: a_sh.btm step_size= 1 year_base= 2020 time_ranges: 2020/03/03 20:16:25 to 2020/03/03 20:46:26 /* whole time range */ 2020-03-03 20:46:45,602 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2020-03-03 20:46:45,604 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2020-03-03 20:46:45,605 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,605 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/cal/botmtrk 2020-03-03 20:46:45,605 DEBUG quick_setup running python command "refabsbt" 2020-03-03 20:46:45,605 DEBUG quick_subs fix_file_type: simple reference_file: a_sh.btm fix_file: ../../nav/a_sh.agt output: a_sh.ref year_base= 2020 ensemble_length= 300 gap_tolerance= 60 2020-03-03 20:46:45,605 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2020-03-03 20:46:45,608 INFO quick_run ...bottom track info in check cal/botmtrk 2020-03-03 20:46:45,608 DEBUG quick_mpl Starting plot: btcal 2020-03-03 20:46:45,609 DEBUG quick_mpl No data in a_sh.btm 2020-03-03 20:46:45,609 DEBUG quick_mpl Returning from Btplot with no output 2020-03-03 20:46:45,609 DEBUG quick_mpl Ending plot: btcal 2020-03-03 20:46:45,609 DEBUG quick_setup nav/as_nav.tmp exists 2020-03-03 20:46:45,609 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,609 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/nav 2020-03-03 20:46:45,610 DEBUG quick_setup running python command "as_nav" 2020-03-03 20:46:45,610 DEBUG quick_subs dbname: ../adcpdb/a_sh output: a_sh step_size: 1 ndepth: 20 time_ranges: separate year_base= 2020 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 2020/03/03 20:16:25 to 2020/03/03 20:46:26 /* the whole time range */ 2020-03-03 20:46:45,610 DEBUG quick_setup about to run adcpsect as_nav.tmp 2020-03-03 20:46:45,613 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2020-03-03 20:46:45,614 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,614 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/cal/watertrk 2020-03-03 20:46:45,614 DEBUG quick_setup running python command "timslip" 2020-03-03 20:46:45,614 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_sh.agt reference_file: ../../nav/a_sh.nav output_file: a_sh_7.cal year_base= 2020 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 2020-03-03 20:46:45,614 DEBUG quick_setup about to run timslip timslip.tmp 2020-03-03 20:46:45,617 INFO quick_run ... watertrack info in cal/watertrk 2020-03-03 20:46:45,618 DEBUG quick_mpl Starting plot: wtcal 2020-03-03 20:46:45,619 DEBUG quick_mpl Found 0 calibration points 2020-03-03 20:46:45,619 DEBUG quick_mpl Fewer than 2 edited points found. No WT plot made. 2020-03-03 20:46:45,619 DEBUG quick_mpl Ending plot: wtcal 2020-03-03 20:46:45,619 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,619 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/cal/watertrk 2020-03-03 20:46:45,619 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2020-03-03 20:46:45,619 DEBUG quick_npy Starting: guess_xducerxy 2020-03-03 20:46:45,660 DEBUG quick_npy Ending: guess_xducerxy 2020-03-03 20:46:45,660 INFO quick_run ... check cal/watertrk for estimate 2020-03-03 20:46:45,660 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:45,661 INFO quick_adcp step 13: extract and plot temperature 2020-03-03 20:46:45,661 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,661 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/edit 2020-03-03 20:46:45,661 DEBUG quick_setup running python command "lst_temp" 2020-03-03 20:46:45,661 DEBUG quick_subs dbname: ../adcpdb/a_sh output: a_sh.tem step_size= 1 year_base= 2020 time_ranges: all 2020-03-03 20:46:45,661 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2020-03-03 20:46:45,664 DEBUG quick_mpl Starting plot: temp 2020-03-03 20:46:45,665 DEBUG quick_mpl plotting 7 points 2020-03-03 20:46:45,774 DEBUG quick_mpl Ending plot: temp 2020-03-03 20:46:45,774 INFO quick_run plotted temperature 2020-03-03 20:46:45,774 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:45,774 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2020-03-03 20:46:45,774 DEBUG quick_setup edit/lst_npings.tmp exists 2020-03-03 20:46:45,774 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,774 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/edit 2020-03-03 20:46:45,774 DEBUG quick_setup running python command "lst_npings" 2020-03-03 20:46:45,774 DEBUG quick_subs dbname: ../adcpdb/a_sh output: a_sh_npings.txt step_size= 1 year_base= 2020 time_ranges: all 2020-03-03 20:46:45,774 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2020-03-03 20:46:45,777 DEBUG quick_mpl Starting plot: npings 2020-03-03 20:46:45,778 DEBUG quick_mpl plotting 7 points 2020-03-03 20:46:45,852 DEBUG quick_mpl Ending plot: npings 2020-03-03 20:46:45,852 INFO quick_run ... plotted number of pings per ensemble 2020-03-03 20:46:45,852 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:45,852 INFO quick_adcp step 15: extract matlab "allbins" 2020-03-03 20:46:45,852 DEBUG quick_asect step 18: make matlab files for plotting 2020-03-03 20:46:45,852 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,852 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/vector 2020-03-03 20:46:45,852 DEBUG quick_setup running python command "timegrid" 2020-03-03 20:46:45,852 DEBUG quick_setup about to run timegrid a_sh.tmp 2020-03-03 20:46:45,855 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,855 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/vector 2020-03-03 20:46:45,855 DEBUG quick_setup running python command "as_vect" 2020-03-03 20:46:45,856 DEBUG quick_setup about to run adcpsect as_vect.tmp 2020-03-03 20:46:45,859 DEBUG quick_asect done making vector matfiles 2020-03-03 20:46:45,859 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,859 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/contour 2020-03-03 20:46:45,859 DEBUG quick_setup running python command "timegrid" 2020-03-03 20:46:45,859 DEBUG quick_setup about to run timegrid a_sh.tmp 2020-03-03 20:46:45,862 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,862 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/contour 2020-03-03 20:46:45,862 DEBUG quick_setup running python command "as_cont" 2020-03-03 20:46:45,862 DEBUG quick_setup about to run adcpsect as_cont.tmp 2020-03-03 20:46:45,866 DEBUG quick_setup starting in /home/data/sh-test-2020-01-02a/proc/os75bb 2020-03-03 20:46:45,866 DEBUG quick_setup executing commands from /home/data/sh-test-2020-01-02a/proc/os75bb/contour 2020-03-03 20:46:45,866 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_sh 2020-03-03 20:46:45,870 DEBUG quick_asect done running getmat with "allbins" 2020-03-03 20:46:45,870 INFO quick_adcp --------------------------------------------- 2020-03-03 20:46:45,870 INFO quick_adcp writing "cruise_info.txt" 2020-03-03 20:46:45,871 INFO run_quick copying NOFIG to /home/adcp/www/figures/os75bb_hcorr_plot.png 2020-03-03 20:46:45,872 INFO run_quick copying NOFIG to /home/adcp/www/figures/thumbnails/os75bb_hcorr_plot_thumb.png 2020-03-03 20:46:45,872 DEBUG run_quick matfile is contour/contour_uv.mat 2020-03-03 20:46:45,872 INFO run_quick copying contour/contour_uv.mat to /home/adcp/www/data/os75bb_cont_uv.mat 2020-03-03 20:46:45,872 DEBUG run_quick matfile is vector/vector_uv.mat 2020-03-03 20:46:45,872 INFO run_quick copying vector/vector_uv.mat to /home/adcp/www/data/os75bb_vect_uv.mat 2020-03-03 20:46:45,872 DEBUG run_quick matfile is contour/contour_xy.mat 2020-03-03 20:46:45,872 INFO run_quick copying contour/contour_xy.mat to /home/adcp/www/data/os75bb_cont_xy.mat 2020-03-03 20:46:45,873 DEBUG run_quick matfile is vector/vector_xy.mat 2020-03-03 20:46:45,873 INFO run_quick copying vector/vector_xy.mat to /home/adcp/www/data/os75bb_vect_xy.mat 2020-03-03 20:46:45,873 DEBUG run_quick about to copy file edit/a_sh.tem to /home/adcp/www/data/os75bb_temp.asc 2020-03-03 20:46:45,873 INFO run_quick copying edit/a_sh.tem to /home/adcp/www/data/os75bb_temp.asc 2020-03-03 20:46:45,901 DEBUG run_quick about to copy netcdf file /home/data/sh-test-2020-01-02a/proc/os75bb/contour/os75bb.nc to /home/adcp/www/data/os75bb.nc 2020-03-03 20:46:45,901 INFO run_quick copying /home/data/sh-test-2020-01-02a/proc/os75bb/contour/os75bb.nc to /home/adcp/www/data/os75bb.nc 2020-03-03 20:46:45,901 INFO run_quick nc_compressed: ddstep is 1 2020-03-03 20:46:45,922 INFO run_quick success: made compressed nc file /home/adcp/uhdas_tmp/os75bb_compr.nc 2020-03-03 20:46:45,927 INFO run_quick generating pingstats for os75bb 2020-03-03 20:46:45,927 INFO run_quick Ending quick_adcp.py