2018-12-19 11:51:13,345 DEBUG run_quick about to write control file parameters to --yearbase 2018 --cruisename WS18351_Kelble --configtype python --sonar os75nb --dbname a_ws --datatype uhdas --cfgpath /home/data/WS18351_Kelble/proc/os75nb/config --ens_len 300 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea # xducer_dx, xducer_dy not set ## see config/WS18351_Kelble_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 2018-12-19 11:51:13,346 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d os75nb 2018-12-19 11:51:13,347 DEBUG quick_setup found cruise_info.hcorr (posmv, pmv, 0) 2018-12-19 11:51:13,347 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2018-12-19 11:51:13,347 INFO quick_setup fix file is a_ws.gps 2018-12-19 11:51:13,347 INFO quick_setup reflayer: ref_method = refsm 2018-12-19 11:51:13,347 INFO quick_setup reflayer: refuv_source = nav 2018-12-19 11:51:13,347 INFO quick_setup reflayer: refuv_smoothwin = 3 2018-12-19 11:51:13,347 INFO quick_adcp ===================================================== 2018-12-19 11:51:13,347 INFO quick_adcp ===================================================== 2018-12-19 11:51:13,347 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d os75nb 2018-12-19 11:51:13,347 INFO quick_adcp cwd is /home/data/WS18351_Kelble/proc/os75nb 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 2018-12-19 11:51:13,347 DEBUG quick_asect extracting matlab files for os75nb 2018-12-19 11:51:13,349 DEBUG quick_setup data directory: /home/data/WS18351_Kelble/raw/os75 2018-12-19 11:51:13,349 INFO quick_setup found 22 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/WS18351_Kelble/raw/os75/*.raw" 2018-12-19 11:51:13,349 INFO quick_setup presently in scan, writing filelist to /home/data/WS18351_Kelble/proc/os75nb/ping/datafile_list.txt 2018-12-19 11:51:13,349 INFO quick_setup found 22 raw data files 2018-12-19 11:51:13,349 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/WS18351_Kelble/raw/os75/ws2018_350_57934.raw ... 2018-12-19 11:51:13,350 DEBUG quick_adcp Wed Dec 19 11:51:13 2018 running: /usr/local/currents/bin/run_quick.py -d os75nb ----- adcpsect variables ------ cbasename contour dbname a_ws 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 25 gridnum 80 increment 10 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/WS18351_Kelble/proc/os75nb/config cntfile /home/data/WS18351_Kelble/proc/os75nb/os75nb_qpy.cnt commands None configtype python cruisename WS18351_Kelble data_def vmadcp.def data_filelist /home/data/WS18351_Kelble/proc/os75nb/ping/datafile_list.txt datadir /home/data/WS18351_Kelble/raw/os75 datafile_glob *.raw datatype uhdas dbname a_ws dday_bailout None debug False ens_len 300 expert None filelist ['/home/data/WS18351_Kelble/raw/os75/ws2018_350_57934.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_350_64800.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_350_72000.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_350_79200.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_00000.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_07200.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_14400.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_21600.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_28800.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_36000.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_43200.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_50400.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_57600.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_64800.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_72000.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_351_79200.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_352_00000.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_352_07200.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_352_14400.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_352_21600.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_352_28800.raw', '/home/data/WS18351_Kelble/raw/os75/ws2018_352_36000.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 25 fixfile a_ws.gps fixfilexy a_ws.gps 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 nb printformats png proc_engine python proc_yearbase 2018 procdir /home/data/WS18351_Kelble/proc/os75nb py_gbindirbase /home/data/WS18351_Kelble/gbin ref_method refsm refuv_inputfile a_ws.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 os75nb 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_ws.gps ub_type 1920 uhdas_config yearbase = 2018 uhdas_dir = /home/data/WS18351_Kelble sonar = os75nb gbin = /home/data/WS18351_Kelble/gbin gbinsonar = /home/data/WS18351_Kelble/gbin/os75 raw = /home/data/WS18351_Kelble/raw rawsonar = /home/data/WS18351_Kelble/raw/os75 rbin = /home/data/WS18351_Kelble/rbin proc = /home/data/WS18351_Kelble/proc procsonar = /home/data/WS18351_Kelble/proc/os75nb 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', 0.0] acc_heading_cutoff = 0.05 update_gbin False uvwref_end None uvwref_start None 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 2018-12-19 11:51:13,350 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:13,350 INFO quick_adcp step 1: set up files in "edit" directory 2018-12-19 11:51:13,350 INFO quick_run file exists (edit/clearflags.tmp). not writing 2018-12-19 11:51:13,350 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:13,350 INFO quick_adcp step 2: scan files for time range 2018-12-19 11:51:13,350 DEBUG quick_npy Starting: scanping 2018-12-19 11:51:13,364 DEBUG quick_npy Ending: scanping 2018-12-19 11:51:13,367 DEBUG quick_subs start_end_time 2018/12/17 16:05:40 to 2018/12/17 16:10:47 2018-12-19 11:51:13,367 DEBUG quick_subs dd0: 350.670602 dd1: 350.674155 2018-12-19 11:51:13,367 DEBUG quick_subs running external command "lstblock adcpdb/a_ws adcpdb/a_ws.lst" 2018-12-19 11:51:13,370 DEBUG quick_subs lstblock ran successfully. 2018-12-19 11:51:13,370 DEBUG quick_subs start_end_time 2018/12/17 16:10:39 to 2018/12/19 11:45:39 2018-12-19 11:51:13,371 DEBUG quick_subs dd0: 350.674062 dd1: 352.490035 2018-12-19 11:51:13,371 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2018-12-19 11:51:13,371 DEBUG quick_adcp origdb_time_range is 2018/12/17 16:10:39 to 2018/12/19 11:45:39 2018-12-19 11:51:13,371 DEBUG quick_adcp (350.674062 to 352.490035) 2018-12-19 11:51:13,371 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:13,371 INFO quick_adcp step 3: generate averaged data... 2018-12-19 11:51:13,371 INFO quick_run file load/ping_editparams.txt exists. not replacing 2018-12-19 11:51:13,371 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:13,371 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/load 2018-12-19 11:51:13,371 DEBUG quick_setup running python command "run_pingavg_npy" 2018-12-19 11:51:13,371 DEBUG quick_npy Starting: pingavg 2018-12-19 11:51:13,372 DEBUG quick_npy xducerxy is [0, 0] 2018-12-19 11:51:13,372 DEBUG quick_npy uvwref is None 2018-12-19 11:51:13,373 DEBUG quick_npy singleping editing parameters: 2018-12-19 11:51:13,373 DEBUG quick_npy bigtarget_mab_window : 11 2018-12-19 11:51:13,373 DEBUG quick_npy rl_endbin : 20 2018-12-19 11:51:13,373 DEBUG quick_npy max_search_depth : 2000 2018-12-19 11:51:13,373 DEBUG quick_npy cor_cutoff : 120 2018-12-19 11:51:13,373 DEBUG quick_npy ampfilt : 40 2018-12-19 11:51:13,373 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2018-12-19 11:51:13,373 DEBUG quick_npy rl_startbin : 2 2018-12-19 11:51:13,373 DEBUG quick_npy ecutoff : 0.800000 2018-12-19 11:51:13,373 DEBUG quick_npy refavg_valcutoff : 1 2018-12-19 11:51:13,373 DEBUG quick_npy weakprof_percent : 30 2018-12-19 11:51:13,373 DEBUG quick_npy bigtarget_ampthresh : 55 2018-12-19 11:51:13,375 INFO pingavg ---------------- 2018-12-19 11:51:13,375 INFO pingavg sonar is os75nb 2018-12-19 11:51:13,375 INFO pingavg Pingavg.run for time range 352.416706 to 352.493875 2018-12-19 11:51:13,375 INFO pingavg transducer offset: xducer_dx = 0.000, xducer_dy = 0.000 2018-12-19 11:51:13,375 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2018-12-19 11:51:13,375 INFO pingavg ---------------- 2018-12-19 11:51:13,383 DEBUG pingavg Chunk 1 of 1, 352.416706 to 352.493875 2018-12-19 11:51:13,384 DEBUG pingavg Nothing written 2018-12-19 11:51:13,384 DEBUG quick_npy wrote 0 averages 2018-12-19 11:51:13,384 DEBUG quick_npy Ending: pingavg 2018-12-19 11:51:13,384 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:13,384 INFO quick_adcp step 4: load averaged data (to database) 2018-12-19 11:51:13,384 DEBUG quick_subs in del_overlapping: lastblock: 2 lastcmd: 2 delblks: [2] loadblks: [2] 2018-12-19 11:51:13,385 DEBUG quick_subs blockfiles remain; running mkblkdir 2018-12-19 11:51:13,385 DEBUG quick_subs running mkblkdir adcpdb/mkblkdir.tmp 2018-12-19 11:51:13,388 DEBUG quick_run [2] 2018-12-19 11:51:13,388 DEBUG quick_run cmdlist 2018-12-19 11:51:13,388 DEBUG quick_run ['./ens_blk002.cmd'] 2018-12-19 11:51:13,390 INFO quick_run loaded time range: 2018/12/18 17:10:36 to 2018/12/19 11:50:38 2018-12-19 11:51:13,390 DEBUG quick_setup load/ldcodas.tmp exists 2018-12-19 11:51:13,390 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:13,390 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/load 2018-12-19 11:51:13,390 DEBUG quick_setup running python command "ldcodas" 2018-12-19 11:51:13,390 DEBUG quick_subs filling "thisload" timerange 2018-12-19 11:51:13,391 DEBUG quick_subs in ldcodas 2018-12-19 11:51:13,391 DEBUG quick_subs cmdlist: 2018-12-19 11:51:13,391 DEBUG quick_subs ['./ens_blk002.cmd'] 2018-12-19 11:51:13,391 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_ws DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2018 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk002.cmd 2018-12-19 11:51:13,391 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2018-12-19 11:51:13,409 INFO quick_run 3 block files present 2018-12-19 11:51:13,409 DEBUG quick_subs running external command "lstblock adcpdb/a_ws adcpdb/a_ws.lst" 2018-12-19 11:51:13,411 DEBUG quick_subs lstblock ran successfully. 2018-12-19 11:51:13,412 DEBUG quick_subs start_end_time 2018/12/17 16:10:39 to 2018/12/19 11:50:38 2018-12-19 11:51:13,412 DEBUG quick_subs dd0: 350.674062 dd1: 352.493495 2018-12-19 11:51:13,412 INFO quick_adcp database time range: 2018-12-19 11:51:13,412 INFO quick_adcp 2018/12/17 16:10:39 to 2018/12/19 11:50:38 2018-12-19 11:51:13,412 INFO quick_adcp (350.674062 to 352.493495) 2018-12-19 11:51:13,412 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:13,412 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/adcpdb 2018-12-19 11:51:13,412 DEBUG quick_setup running python command "lst_conf" 2018-12-19 11:51:13,412 DEBUG quick_subs dbname: a_ws output: a_ws.cnh time_ranges: all 2018-12-19 11:51:13,412 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2018-12-19 11:51:13,416 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:13,416 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2018-12-19 11:51:13,417 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2018-12-19 11:51:13,417 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:13,417 INFO quick_adcp step 6: run setflags? 2018-12-19 11:51:13,417 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:13,417 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/edit 2018-12-19 11:51:13,417 DEBUG quick_setup running python command "write_setflags" 2018-12-19 11:51:13,417 DEBUG quick_subs dbname: ../adcpdb/a_ws pg_min: 50 set_range_bit time_ranges: all 2018-12-19 11:51:13,417 DEBUG quick_setup about to run setflags setflags.tmp 2018-12-19 11:51:13,422 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:13,422 INFO quick_adcp step 7: get navigation 2018-12-19 11:51:13,422 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:13,422 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/nav 2018-12-19 11:51:13,422 DEBUG quick_setup running python command "catnav" 2018-12-19 11:51:13,423 INFO quick_subs navigation file nav/a_ws.gps created from load/*.gps2 2018-12-19 11:51:13,423 INFO quick_subs navigation file nav/a_ws.agt created from load/*.gpst2 2018-12-19 11:51:13,423 DEBUG quick_mpl Starting plot: uvship 2018-12-19 11:51:13,656 DEBUG quick_mpl Ending plot: uvship 2018-12-19 11:51:13,656 INFO quick_run plotted uvship 2018-12-19 11:51:13,656 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:13,656 INFO quick_adcp step 8: list heading 2018-12-19 11:51:13,656 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2018-12-19 11:51:13,656 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:13,656 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/cal/rotate 2018-12-19 11:51:13,656 DEBUG quick_setup running python command "lst_hdg" 2018-12-19 11:51:13,656 DEBUG quick_subs dbname: ../../adcpdb/a_ws output: scn.hdg step_size= 1 year_base= 2018 time_ranges: all 2018-12-19 11:51:13,656 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2018-12-19 11:51:13,661 INFO quick_run ... headings extracted 2018-12-19 11:51:13,662 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:13,662 INFO quick_adcp step 9: plot heading correction 2018-12-19 11:51:13,662 DEBUG quick_run hcorr_inst is posmv 2018-12-19 11:51:13,662 DEBUG quick_mpl Starting plot: hcorr 2018-12-19 11:51:13,666 DEBUG quick_mpl found 1.819434 days of data 2018-12-19 11:51:13,666 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2018-12-19 11:51:13,666 DEBUG quick_mpl printing 1 pages 2018-12-19 11:51:13,896 DEBUG quick_mpl Ending plot: hcorr 2018-12-19 11:51:13,896 INFO quick_run plots are in cal/rotate/*png 2018-12-19 11:51:13,896 INFO quick_adcp ------------------------- 2018-12-19 11:51:13,896 INFO quick_adcp ---- running navsteps --- 2018-12-19 11:51:13,897 INFO quick_adcp ------------------------- 2018-12-19 11:51:13,897 INFO quick_adcp step 10: nav steps: run adcpsect 2018-12-19 11:51:13,897 INFO quick_adcp navstep 1 2018-12-19 11:51:13,897 DEBUG quick_setup nav/as_nav.tmp exists 2018-12-19 11:51:13,897 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:13,897 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/nav 2018-12-19 11:51:13,897 DEBUG quick_setup running python command "as_nav" 2018-12-19 11:51:13,897 DEBUG quick_subs dbname: ../adcpdb/a_ws output: a_ws 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 2018/12/17 16:10:39 to 2018/12/19 11:50:38 /* the whole time range */ 2018-12-19 11:51:13,897 DEBUG quick_setup about to run adcpsect as_nav.tmp 2018-12-19 11:51:13,904 INFO quick_run ... ran adcpsect for navsteps 2018-12-19 11:51:13,904 INFO quick_adcp ------------------------- 2018-12-19 11:51:13,904 INFO quick_adcp step 11: nav steps: run refabs 2018-12-19 11:51:13,904 INFO quick_adcp navstep 2 2018-12-19 11:51:13,904 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:13,904 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/nav 2018-12-19 11:51:13,904 DEBUG quick_setup running python command "refabs" 2018-12-19 11:51:13,904 DEBUG quick_subs fix_file_type: simple reference_file: a_ws.nav fix_file: a_ws.gps output: a_ws.ref year_base= 2018 ensemble_length= 300 gap_tolerance= 10 2018-12-19 11:51:13,904 DEBUG quick_setup about to run refabs refabs.tmp 2018-12-19 11:51:13,911 INFO quick_run ... ran refabs for navsteps 2018-12-19 11:51:13,911 INFO quick_adcp ------------------------- 2018-12-19 11:51:13,911 INFO quick_adcp step 12: nav steps: run smoothr for plots 2018-12-19 11:51:13,911 INFO quick_adcp navstep 3 2018-12-19 11:51:13,911 DEBUG quick_setup nav/smoothr.tmp exists 2018-12-19 11:51:13,911 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:13,911 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/nav 2018-12-19 11:51:13,911 DEBUG quick_setup running python command "smoothr" 2018-12-19 11:51:13,911 DEBUG quick_subs reference_file: a_ws.nav refabs_output: a_ws.ref output: a_ws.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 2018-12-19 11:51:13,911 DEBUG quick_setup about to run smoothr smoothr.tmp 2018-12-19 11:51:13,927 INFO quick_run ... ran smoothr 2018-12-19 11:51:13,927 INFO quick_adcp ------------------------- 2018-12-19 11:51:13,927 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2018-12-19 11:51:13,927 INFO quick_adcp navstep 4 2018-12-19 11:51:13,927 INFO quick_run smoothing method for ship speed: refsm 2018-12-19 11:51:13,927 INFO quick_run smoothing window: 3 2018-12-19 11:51:13,927 INFO quick_run ship speed source: nav 2018-12-19 11:51:13,927 DEBUG quick_npy Starting: refsm 2018-12-19 11:51:13,950 DEBUG quick_npy Ending: refsm 2018-12-19 11:51:13,950 INFO quick_run ... shipspeed smoothing step done 2018-12-19 11:51:13,950 INFO quick_adcp ------------------------- 2018-12-19 11:51:13,950 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2018-12-19 11:51:13,950 INFO quick_adcp navstep 5 2018-12-19 11:51:13,950 DEBUG quick_setup nav/put_txy.tmp exists 2018-12-19 11:51:13,950 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:13,950 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/nav 2018-12-19 11:51:13,950 DEBUG quick_setup running python command "put_txy" 2018-12-19 11:51:13,950 DEBUG quick_subs dbname: ../adcpdb/a_ws position_file: a_ws.gps year_base= 2018 tolerance= 5 2018-12-19 11:51:13,950 DEBUG quick_setup about to run put_txy put_txy.tmp 2018-12-19 11:51:13,956 INFO quick_run ... ran put_txy 2018-12-19 11:51:13,956 DEBUG quick_setup nav/put_tuv.tmp exists 2018-12-19 11:51:13,956 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:13,956 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/nav 2018-12-19 11:51:13,957 DEBUG quick_setup running python command "put_tuv" 2018-12-19 11:51:13,957 DEBUG quick_subs dbname: ../adcpdb/a_ws shipspeed_file: refsm_tuv.asc year_base= 2018 tolerance= 5 2018-12-19 11:51:13,957 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2018-12-19 11:51:13,962 INFO quick_run ... ran put_tuv 2018-12-19 11:51:13,962 DEBUG quick_mpl Starting plot: nav 2018-12-19 11:51:14,154 DEBUG quick_mpl Ending plot: nav 2018-12-19 11:51:14,154 INFO quick_run ... made navigation plot 2018-12-19 11:51:14,154 INFO quick_adcp ------------------------- 2018-12-19 11:51:14,154 INFO quick_adcp step 15: nav steps: make reflayer plots 2018-12-19 11:51:14,154 INFO quick_adcp navstep 6 2018-12-19 11:51:14,154 DEBUG quick_mpl Starting plot: refl 2018-12-19 11:51:14,163 DEBUG quick_mpl found 1.815970 days of data 2018-12-19 11:51:14,163 DEBUG quick_mpl start day is 350.000000 2018-12-19 11:51:14,163 DEBUG quick_mpl figures with 2.000000 days per page 2018-12-19 11:51:14,163 DEBUG quick_mpl printing 2 pages 2018-12-19 11:51:14,163 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2018-12-19 11:51:14,643 DEBUG quick_mpl Ending plot: refl 2018-12-19 11:51:14,643 INFO quick_run ... made reflayer plots 2018-12-19 11:51:14,643 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:14,643 INFO quick_adcp step 10: find profile flags 2018-12-19 11:51:14,643 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,643 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/edit 2018-12-19 11:51:14,643 DEBUG quick_setup running python command "run_autoedit_npy" 2018-12-19 11:51:14,643 DEBUG quick_npy Starting: autoedit 2018-12-19 11:51:14,667 DEBUG pingedit wrote 58 bad bins to abadbin_tmp.asc 2018-12-19 11:51:14,669 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2018-12-19 11:51:14,669 DEBUG quick_npy Ending: autoedit 2018-12-19 11:51:14,669 INFO quick_run ... extracted files using automatic editing 2018-12-19 11:51:14,669 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:14,670 INFO quick_adcp step 11: apply editing 2018-12-19 11:51:14,670 DEBUG quick_run starting in: /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,670 DEBUG quick_run executing commands from: edit 2018-12-19 11:51:14,670 DEBUG quick_run about to run dbupdate ../adcpdb/a_ws abadprf_tmp.asc 2018-12-19 11:51:14,674 DEBUG quick_run about to run badbin ../adcpdb/a_ws abadbin_tmp.asc 2018-12-19 11:51:14,679 DEBUG quick_subs dbname: ../adcpdb/a_ws pg_min: 50 set_range_bit time_ranges: all 2018-12-19 11:51:14,679 DEBUG quick_run about to run setflags setflags.tmp 2018-12-19 11:51:14,685 DEBUG quick_run changing directories back to /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,685 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:14,685 INFO quick_adcp step 12: run calibration steps 2018-12-19 11:51:14,685 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2018-12-19 11:51:14,685 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,685 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/cal/botmtrk 2018-12-19 11:51:14,685 DEBUG quick_setup running python command "lst_btrk" 2018-12-19 11:51:14,685 DEBUG quick_subs dbname: ../../adcpdb/a_ws output: a_ws.btm step_size= 1 year_base= 2018 time_ranges: 2018/12/17 16:10:39 to 2018/12/19 11:50:38 /* whole time range */ 2018-12-19 11:51:14,685 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2018-12-19 11:51:14,690 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2018-12-19 11:51:14,690 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,690 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/cal/botmtrk 2018-12-19 11:51:14,690 DEBUG quick_setup running python command "refabsbt" 2018-12-19 11:51:14,690 DEBUG quick_subs fix_file_type: simple reference_file: a_ws.btm fix_file: ../../nav/a_ws.gps output: a_ws.ref year_base= 2018 ensemble_length= 300 gap_tolerance= 60 2018-12-19 11:51:14,690 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2018-12-19 11:51:14,694 INFO quick_run ...bottom track info in check cal/botmtrk 2018-12-19 11:51:14,694 DEBUG quick_mpl Starting plot: btcal 2018-12-19 11:51:14,695 DEBUG quick_mpl No data in a_ws.btm 2018-12-19 11:51:14,695 DEBUG quick_mpl Returning from Btplot with no output 2018-12-19 11:51:14,695 DEBUG quick_mpl Ending plot: btcal 2018-12-19 11:51:14,695 DEBUG quick_setup nav/as_nav.tmp exists 2018-12-19 11:51:14,695 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,695 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/nav 2018-12-19 11:51:14,695 DEBUG quick_setup running python command "as_nav" 2018-12-19 11:51:14,695 DEBUG quick_subs dbname: ../adcpdb/a_ws output: a_ws 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 2018/12/17 16:10:39 to 2018/12/19 11:50:38 /* the whole time range */ 2018-12-19 11:51:14,695 DEBUG quick_setup about to run adcpsect as_nav.tmp 2018-12-19 11:51:14,702 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2018-12-19 11:51:14,702 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,702 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/cal/watertrk 2018-12-19 11:51:14,702 DEBUG quick_setup running python command "timslip" 2018-12-19 11:51:14,702 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_ws.gps reference_file: ../../nav/a_ws.nav output_file: a_ws_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 2018-12-19 11:51:14,702 DEBUG quick_setup about to run timslip timslip.tmp 2018-12-19 11:51:14,708 INFO quick_run ... watertrack info in cal/watertrk 2018-12-19 11:51:14,708 DEBUG quick_mpl Starting plot: wtcal 2018-12-19 11:51:14,709 DEBUG quick_mpl Found 14 calibration points 2018-12-19 11:51:14,709 ERROR quick_mpl Failure in plot: wtcal Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/pycurrents/adcp/quick_mpl.py", line 1854, in run_plotter Plotter() File "/usr/local/lib/python2.7/dist-packages/pycurrents/adcp/quick_mpl.py", line 1529, in __call__ self.print_stats() File "/usr/local/lib/python2.7/dist-packages/pycurrents/adcp/quick_mpl.py", line 1637, in print_stats self.caldat_ma['ph'], 1) File "/usr/lib/python2.7/dist-packages/numpy/lib/polynomial.py", line 559, in polyfit raise TypeError("expected non-empty vector for x") TypeError: expected non-empty vector for x 2018-12-19 11:51:14,710 DEBUG quick_mpl Ending plot: wtcal 2018-12-19 11:51:14,710 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,710 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/cal/watertrk 2018-12-19 11:51:14,710 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2018-12-19 11:51:14,710 DEBUG quick_npy Starting: guess_xducerxy 2018-12-19 11:51:14,727 DEBUG quick_npy Ending: guess_xducerxy 2018-12-19 11:51:14,727 INFO quick_run ... check cal/watertrk for estimate 2018-12-19 11:51:14,727 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:14,727 INFO quick_adcp step 13: extract and plot temperature 2018-12-19 11:51:14,727 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,727 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/edit 2018-12-19 11:51:14,728 DEBUG quick_setup running python command "lst_temp" 2018-12-19 11:51:14,728 DEBUG quick_subs dbname: ../adcpdb/a_ws output: a_ws.tem step_size= 1 year_base= 2018 time_ranges: all 2018-12-19 11:51:14,728 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2018-12-19 11:51:14,733 DEBUG quick_mpl Starting plot: temp 2018-12-19 11:51:14,737 DEBUG quick_mpl plotting 525 points 2018-12-19 11:51:14,872 DEBUG quick_mpl Ending plot: temp 2018-12-19 11:51:14,872 INFO quick_run plotted temperature 2018-12-19 11:51:14,872 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:14,872 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2018-12-19 11:51:14,872 DEBUG quick_setup edit/lst_npings.tmp exists 2018-12-19 11:51:14,872 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,872 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/edit 2018-12-19 11:51:14,872 DEBUG quick_setup running python command "lst_npings" 2018-12-19 11:51:14,872 DEBUG quick_subs dbname: ../adcpdb/a_ws output: a_ws_npings.txt step_size= 1 year_base= 2018 time_ranges: all 2018-12-19 11:51:14,873 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2018-12-19 11:51:14,878 DEBUG quick_mpl Starting plot: npings 2018-12-19 11:51:14,881 DEBUG quick_mpl plotting 525 points 2018-12-19 11:51:14,965 DEBUG quick_mpl Ending plot: npings 2018-12-19 11:51:14,965 INFO quick_run ... plotted number of pings per ensemble 2018-12-19 11:51:14,965 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:14,965 INFO quick_adcp step 15: extract matlab "allbins" 2018-12-19 11:51:14,965 DEBUG quick_asect step 18: make matlab files for plotting 2018-12-19 11:51:14,965 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,965 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/vector 2018-12-19 11:51:14,965 DEBUG quick_setup running python command "timegrid" 2018-12-19 11:51:14,965 DEBUG quick_setup about to run timegrid a_ws.tmp 2018-12-19 11:51:14,970 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,970 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/vector 2018-12-19 11:51:14,970 DEBUG quick_setup running python command "as_vect" 2018-12-19 11:51:14,970 DEBUG quick_setup about to run adcpsect as_vect.tmp 2018-12-19 11:51:14,977 DEBUG quick_asect done making vector matfiles 2018-12-19 11:51:14,977 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,977 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/contour 2018-12-19 11:51:14,977 DEBUG quick_setup running python command "timegrid" 2018-12-19 11:51:14,977 DEBUG quick_setup about to run timegrid a_ws.tmp 2018-12-19 11:51:14,981 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,982 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/contour 2018-12-19 11:51:14,982 DEBUG quick_setup running python command "as_cont" 2018-12-19 11:51:14,982 DEBUG quick_setup about to run adcpsect as_cont.tmp 2018-12-19 11:51:14,992 DEBUG quick_setup starting in /home/data/WS18351_Kelble/proc/os75nb 2018-12-19 11:51:14,992 DEBUG quick_setup executing commands from /home/data/WS18351_Kelble/proc/os75nb/contour 2018-12-19 11:51:14,992 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_ws 2018-12-19 11:51:15,009 DEBUG quick_asect done running getmat with "allbins" 2018-12-19 11:51:15,009 INFO quick_adcp --------------------------------------------- 2018-12-19 11:51:15,009 INFO quick_adcp writing "cruise_info.txt" 2018-12-19 11:51:15,010 INFO run_quick copying NOFIG to /home/adcp/www/figures/os75nb_hcorr_plot.png 2018-12-19 11:51:15,010 INFO run_quick copying NOFIG to /home/adcp/www/figures/thumbnails/os75nb_hcorr_plot_thumb.png 2018-12-19 11:51:15,010 DEBUG run_quick matfile is contour/contour_uv.mat 2018-12-19 11:51:15,011 INFO run_quick copying contour/contour_uv.mat to /home/adcp/www/data/os75nb_cont_uv.mat 2018-12-19 11:51:15,011 DEBUG run_quick matfile is vector/vector_uv.mat 2018-12-19 11:51:15,011 INFO run_quick copying vector/vector_uv.mat to /home/adcp/www/data/os75nb_vect_uv.mat 2018-12-19 11:51:15,011 DEBUG run_quick matfile is contour/contour_xy.mat 2018-12-19 11:51:15,011 INFO run_quick copying contour/contour_xy.mat to /home/adcp/www/data/os75nb_cont_xy.mat 2018-12-19 11:51:15,011 DEBUG run_quick matfile is vector/vector_xy.mat 2018-12-19 11:51:15,011 INFO run_quick copying vector/vector_xy.mat to /home/adcp/www/data/os75nb_vect_xy.mat 2018-12-19 11:51:15,011 DEBUG run_quick about to copy file edit/a_ws.tem to /home/adcp/www/data/os75nb_temp.asc 2018-12-19 11:51:15,011 INFO run_quick copying edit/a_ws.tem to /home/adcp/www/data/os75nb_temp.asc 2018-12-19 11:51:15,058 DEBUG run_quick about to copy netcdf file /home/data/WS18351_Kelble/proc/os75nb/contour/os75nb.nc to /home/adcp/www/data/os75nb.nc 2018-12-19 11:51:15,059 INFO run_quick copying /home/data/WS18351_Kelble/proc/os75nb/contour/os75nb.nc to /home/adcp/www/data/os75nb.nc 2018-12-19 11:51:15,059 INFO run_quick nc_compressed: ddstep is 1 2018-12-19 11:51:15,091 INFO run_quick success: made compressed nc file /home/adcp/uhdas_tmp/os75nb_compr.nc 2018-12-19 11:51:15,097 INFO run_quick generating pingstats for os75nb 2018-12-19 11:51:15,097 INFO run_quick Ending quick_adcp.py