2017-09-03 18:06:54,751 DEBUG root about to write control file parameters to --yearbase 2017 --cruisename AR22 --configtype python --sonar os38nb --dbname a_ar --datatype uhdas --cfgpath /home/data/AR22/proc/os38nb/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 6 --xducer_dy 12 ## see config/AR22_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 2017-09-03 18:06:54,751 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d os38nb 2017-09-03 18:06:54,752 DEBUG quick_setup found cruise_info.hcorr (posmv, pmv, 0) 2017-09-03 18:06:54,752 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2017-09-03 18:06:54,753 INFO quick_setup fix file is a_ar.gps 2017-09-03 18:06:54,753 INFO quick_setup reflayer: ref_method = refsm 2017-09-03 18:06:54,753 INFO quick_setup reflayer: refuv_source = nav 2017-09-03 18:06:54,753 INFO quick_setup reflayer: refuv_smoothwin = 3 2017-09-03 18:06:54,753 INFO quick_adcp importing numpy version 1.11.0 2017-09-03 18:06:54,760 INFO quick_adcp importing matplotlib version 1.5.1 2017-09-03 18:06:54,899 DEBUG quick_mpl in Q_mpl 2017-09-03 18:06:54,899 INFO quick_adcp ===================================================== 2017-09-03 18:06:54,899 INFO quick_adcp ===================================================== 2017-09-03 18:06:54,899 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d os38nb 2017-09-03 18:06:54,899 INFO quick_adcp cwd is /home/data/AR22/proc/os38nb 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 2017-09-03 18:06:54,899 DEBUG quick_asect extracting matlab files for os38nb 2017-09-03 18:06:54,900 DEBUG quick_setup data directory: /home/data/AR22/raw/os38 2017-09-03 18:06:54,900 INFO quick_setup found 17 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/AR22/raw/os38/*.raw" 2017-09-03 18:06:54,901 INFO quick_setup presently in scan, writing filelist to /home/data/AR22/proc/os38nb/ping/datafile_list.txt 2017-09-03 18:06:54,901 INFO quick_setup found 17 raw data files 2017-09-03 18:06:54,901 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/AR22/raw/os38/ar2017_244_44651.raw ... 2017-09-03 18:06:54,901 DEBUG quick_adcp Sun Sep 3 18:06:54 2017 running quick_adcp.py as follows: --cntfile /home/data/AR22/proc/os38nb/os38nb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_ar 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 43 gridnum 80 increment 20 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2017 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/AR22/proc/os38nb/config cntfile /home/data/AR22/proc/os38nb/os38nb_qpy.cnt commands None configtype python cruisename AR22 data_def vmadcp.def data_filelist /home/data/AR22/proc/os38nb/ping/datafile_list.txt datadir /home/data/AR22/raw/os38 datafile_glob *.raw datatype uhdas dbname a_ar dday_bailout None debug False ens_len 300 expert None filelist ['/home/data/AR22/raw/os38/ar2017_244_44651.raw', '/home/data/AR22/raw/os38/ar2017_244_50400.raw', '/home/data/AR22/raw/os38/ar2017_244_57600.raw', '/home/data/AR22/raw/os38/ar2017_244_61927.raw', '/home/data/AR22/raw/os38/ar2017_244_64800.raw', '/home/data/AR22/raw/os38/ar2017_244_73796.raw', '/home/data/AR22/raw/os38/ar2017_244_79200.raw', '/home/data/AR22/raw/os38/ar2017_245_00000.raw', '/home/data/AR22/raw/os38/ar2017_245_07200.raw', '/home/data/AR22/raw/os38/ar2017_245_14400.raw', '/home/data/AR22/raw/os38/ar2017_245_21600.raw', '/home/data/AR22/raw/os38/ar2017_245_28800.raw', '/home/data/AR22/raw/os38/ar2017_245_36000.raw', '/home/data/AR22/raw/os38/ar2017_245_43200.raw', '/home/data/AR22/raw/os38/ar2017_245_50400.raw', '/home/data/AR22/raw/os38/ar2017_245_57600.raw', '/home/data/AR22/raw/os38/ar2017_245_64800.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 43 fixfile a_ar.gps fixfilexy a_ar.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 nb printformats png proc_engine python proc_yearbase 2017 procdir /home/data/AR22/proc/os38nb py_gbindirbase /home/data/AR22/gbin ref_method refsm refuv_inputfile a_ar.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 os38nb steps2rerun sum_xducer_dx 6 sum_xducer_dy 12 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_ar.agt ub_type 1920 uhdas_config yearbase = 2017 uhdas_dir = /home/data/AR22 sonar = os38nb gbin = /home/data/AR22/gbin gbinsonar = /home/data/AR22/gbin/os38 raw = /home/data/AR22/raw rawsonar = /home/data/AR22/raw/os38 rbin = /home/data/AR22/rbin proc = /home/data/AR22/proc procsonar = /home/data/AR22/proc/os38nb other attributes: gbin_params = hdg_inst : gyro hdg_inst_msgs : [('gyro', 'hdg'), ('posmv', 'pmv'), ('gyro2', 'hdg')] hdg_msg : hdg pitch_inst : posmv pitch_msg : pmv pos_inst : cnav pos_msg : gps roll_inst : posmv roll_msg : pmv hcorr = ['posmv', 'pmv', 0.0] acc_heading_cutoff = 0.02 update_gbin False uvwref_end None uvwref_start None vardoc False varvals False wtrk_step 7 xducer_dx 6 xducer_dy 12 yearbase 2017 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 2017-09-03 18:06:54,901 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:54,901 INFO quick_adcp step 1: set up files in "edit" directory 2017-09-03 18:06:54,901 INFO quick_run file exists (edit/clearflags.tmp). not writing 2017-09-03 18:06:54,901 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:54,901 INFO quick_adcp step 2: scan files for time range 2017-09-03 18:06:54,901 DEBUG quick_npy Starting: scanping 2017-09-03 18:06:54,911 DEBUG quick_npy Ending: scanping 2017-09-03 18:06:54,912 DEBUG quick_subs start_end_time 2017/09/02 12:24:15 to 2017/09/02 12:29:27 2017-09-03 18:06:54,912 DEBUG quick_subs dd0: 244.516840 dd1: 244.520451 2017-09-03 18:06:54,912 INFO quick_adcp looking for database with adcpdb/a_ar*.blk 2017-09-03 18:06:54,912 INFO quick_adcp database found: listing blocks 2017-09-03 18:06:54,912 DEBUG quick_subs removing a_ardir.blk 2017-09-03 18:06:54,912 DEBUG quick_subs about to run mkblkdir 2017-09-03 18:06:54,912 DEBUG quick_subs database still exists; rerunning mkdirblk 2017-09-03 18:06:54,912 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2017-09-03 18:06:54,917 DEBUG quick_subs database passes. 2017-09-03 18:06:54,917 DEBUG quick_subs start_end_time 2017/09/02 12:29:12 to 2017/09/03 17:59:57 2017-09-03 18:06:54,917 DEBUG quick_subs dd0: 244.520278 dd1: 245.749965 2017-09-03 18:06:54,917 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2017-09-03 18:06:54,917 DEBUG quick_adcp origdb_time_range is 2017/09/02 12:29:12 to 2017/09/03 17:59:57 2017-09-03 18:06:54,917 DEBUG quick_adcp (244.520278 to 245.749965) 2017-09-03 18:06:54,917 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:54,917 INFO quick_adcp step 3: generate averaged data... 2017-09-03 18:06:54,917 INFO quick_run file load/ping_editparams.txt exists. not replacing 2017-09-03 18:06:54,917 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:54,917 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/load 2017-09-03 18:06:54,917 DEBUG quick_setup running python command "run_pingavg_npy" 2017-09-03 18:06:54,917 DEBUG quick_npy Starting: pingavg 2017-09-03 18:06:54,918 DEBUG quick_npy xducerxy is [6, 12] 2017-09-03 18:06:54,918 DEBUG quick_npy uvwref is None 2017-09-03 18:06:54,919 DEBUG quick_npy singleping editing parameters: 2017-09-03 18:06:54,919 DEBUG quick_npy bigtarget_mab_window : 11 2017-09-03 18:06:54,919 DEBUG quick_npy rl_endbin : 20 2017-09-03 18:06:54,919 DEBUG quick_npy max_search_depth : 2000 2017-09-03 18:06:54,919 DEBUG quick_npy cor_cutoff : 120 2017-09-03 18:06:54,919 DEBUG quick_npy ampfilt : 40 2017-09-03 18:06:54,919 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2017-09-03 18:06:54,919 DEBUG quick_npy rl_startbin : 2 2017-09-03 18:06:54,919 DEBUG quick_npy ecutoff : 0.800000 2017-09-03 18:06:54,919 DEBUG quick_npy refavg_valcutoff : 1 2017-09-03 18:06:54,919 DEBUG quick_npy weakprof_percent : 30 2017-09-03 18:06:54,919 DEBUG quick_npy bigtarget_ampthresh : 55 2017-09-03 18:06:54,920 INFO pingavg ---------------- 2017-09-03 18:06:54,921 INFO pingavg sonar is os38nb 2017-09-03 18:06:54,921 INFO pingavg Pingavg.run for time range 245.749998 to 245.753644 2017-09-03 18:06:54,921 INFO pingavg transducer offset: xducer_dx = 6.000, xducer_dy = 12.000 2017-09-03 18:06:54,921 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2017-09-03 18:06:54,921 INFO pingavg ---------------- 2017-09-03 18:06:54,928 DEBUG pingavg Chunk 1 of 1, 245.749998 to 245.753644 2017-09-03 18:06:54,928 DEBUG pingavg Nothing written 2017-09-03 18:06:54,928 DEBUG quick_npy wrote 0 averages 2017-09-03 18:06:54,928 DEBUG quick_npy Ending: pingavg 2017-09-03 18:06:54,928 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:54,928 INFO quick_adcp step 4: load averaged data (to database) 2017-09-03 18:06:54,928 DEBUG quick_subs in del_overlapping 2017-09-03 18:06:54,928 DEBUG quick_subs lastblock: 2017-09-03 18:06:54,928 DEBUG quick_subs 3 2017-09-03 18:06:54,928 DEBUG quick_subs lastcmd: 2017-09-03 18:06:54,928 DEBUG quick_subs 3 2017-09-03 18:06:54,928 DEBUG quick_subs delblks: 2017-09-03 18:06:54,928 DEBUG quick_subs [3] 2017-09-03 18:06:54,928 DEBUG quick_subs loadblks: 2017-09-03 18:06:54,929 DEBUG quick_subs [3] 2017-09-03 18:06:54,929 DEBUG quick_subs about to run mkblkdir 2017-09-03 18:06:54,929 DEBUG quick_subs database still exists; rerunning mkdirblk 2017-09-03 18:06:54,929 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2017-09-03 18:06:54,933 DEBUG quick_subs database passes. 2017-09-03 18:06:54,933 DEBUG quick_subs start_end_time 2017/09/02 12:29:12 to 2017/09/02 18:02:44 2017-09-03 18:06:54,933 DEBUG quick_subs dd0: 244.520278 dd1: 244.751898 2017-09-03 18:06:54,933 DEBUG quick_run [3] 2017-09-03 18:06:54,933 DEBUG quick_run cmdlist 2017-09-03 18:06:54,933 DEBUG quick_run ['./ens_blk003.cmd'] 2017-09-03 18:06:54,934 INFO quick_run loaded time range: 2017/09/02 20:34:56 to 2017/09/03 18:04:57 2017-09-03 18:06:54,934 DEBUG quick_setup load/ldcodas.tmp exists 2017-09-03 18:06:54,934 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:54,934 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/load 2017-09-03 18:06:54,934 DEBUG quick_setup running python command "ldcodas" 2017-09-03 18:06:54,935 DEBUG quick_subs filling "thisload" timerange 2017-09-03 18:06:54,935 DEBUG quick_subs in ldcodas 2017-09-03 18:06:54,935 DEBUG quick_subs cmdlist: 2017-09-03 18:06:54,935 DEBUG quick_subs ['./ens_blk003.cmd'] 2017-09-03 18:06:54,935 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_ar DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2017 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk003.cmd 2017-09-03 18:06:54,935 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2017-09-03 18:06:54,951 INFO quick_run 4 block files present 2017-09-03 18:06:54,951 DEBUG quick_subs removing a_ardir.blk 2017-09-03 18:06:54,952 DEBUG quick_subs about to run mkblkdir 2017-09-03 18:06:54,952 DEBUG quick_subs database still exists; rerunning mkdirblk 2017-09-03 18:06:54,952 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2017-09-03 18:06:54,956 DEBUG quick_subs database passes. 2017-09-03 18:06:54,956 DEBUG quick_subs start_end_time 2017/09/02 12:29:12 to 2017/09/03 18:04:57 2017-09-03 18:06:54,956 DEBUG quick_subs dd0: 244.520278 dd1: 245.753437 2017-09-03 18:06:54,956 INFO quick_adcp database time range: 2017-09-03 18:06:54,956 INFO quick_adcp 2017/09/02 12:29:12 to 2017/09/03 18:04:57 2017-09-03 18:06:54,956 INFO quick_adcp (244.520278 to 245.753437) 2017-09-03 18:06:54,956 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:54,956 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/adcpdb 2017-09-03 18:06:54,956 DEBUG quick_setup running python command "lst_conf" 2017-09-03 18:06:54,956 DEBUG quick_subs dbname: a_ar output: a_ar.cnh time_ranges: all 2017-09-03 18:06:54,956 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2017-09-03 18:06:54,959 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:54,959 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2017-09-03 18:06:54,959 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2017-09-03 18:06:54,959 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:54,959 INFO quick_adcp step 6: run setflags? 2017-09-03 18:06:54,960 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:54,960 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/edit 2017-09-03 18:06:54,960 DEBUG quick_setup running python command "write_setflags" 2017-09-03 18:06:54,960 DEBUG quick_subs dbname: ../adcpdb/a_ar pg_min: 50 set_range_bit time_ranges: all 2017-09-03 18:06:54,960 DEBUG quick_setup about to run setflags setflags.tmp 2017-09-03 18:06:54,963 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:54,963 INFO quick_adcp step 7: get navigation 2017-09-03 18:06:54,963 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:54,963 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/nav 2017-09-03 18:06:54,963 DEBUG quick_setup running python command "catnav" 2017-09-03 18:06:54,963 INFO quick_subs navigation file nav/a_ar.gps created from load/*.gps2 2017-09-03 18:06:54,964 INFO quick_subs navigation file nav/a_ar.agt created from load/*.gpst2 2017-09-03 18:06:54,964 DEBUG quick_mpl Starting plot: uvship 2017-09-03 18:06:55,157 DEBUG quick_mpl Ending plot: uvship 2017-09-03 18:06:55,157 INFO quick_run plotted uvship 2017-09-03 18:06:55,157 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:55,157 INFO quick_adcp step 8: list heading 2017-09-03 18:06:55,157 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2017-09-03 18:06:55,158 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,158 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/cal/rotate 2017-09-03 18:06:55,158 DEBUG quick_setup running python command "lst_hdg" 2017-09-03 18:06:55,158 DEBUG quick_subs dbname: ../../adcpdb/a_ar output: scn.hdg step_size= 1 year_base= 2017 time_ranges: all 2017-09-03 18:06:55,158 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2017-09-03 18:06:55,162 INFO quick_run ... headings extracted 2017-09-03 18:06:55,162 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:55,162 INFO quick_adcp step 9: plot heading correction 2017-09-03 18:06:55,162 DEBUG quick_run hcorr_inst is posmv 2017-09-03 18:06:55,162 DEBUG quick_mpl Starting plot: hcorr 2017-09-03 18:06:55,164 DEBUG quick_mpl found 1.233160 days of data 2017-09-03 18:06:55,165 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2017-09-03 18:06:55,165 DEBUG quick_mpl printing 1 pages 2017-09-03 18:06:55,350 DEBUG quick_mpl Ending plot: hcorr 2017-09-03 18:06:55,350 INFO quick_run plots are in cal/rotate/*png 2017-09-03 18:06:55,351 INFO quick_adcp ------------------------- 2017-09-03 18:06:55,351 INFO quick_adcp ---- running navsteps --- 2017-09-03 18:06:55,351 INFO quick_adcp ------------------------- 2017-09-03 18:06:55,351 INFO quick_adcp step 10: nav steps: run adcpsect 2017-09-03 18:06:55,351 INFO quick_adcp navstep 1 2017-09-03 18:06:55,351 DEBUG quick_setup nav/as_nav.tmp exists 2017-09-03 18:06:55,351 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,351 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/nav 2017-09-03 18:06:55,351 DEBUG quick_setup running python command "as_nav" 2017-09-03 18:06:55,351 DEBUG quick_subs dbname: ../adcpdb/a_ar output: a_ar step_size: 1 ndepth: 20 time_ranges: separate year_base= 2017 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 2017/09/02 12:29:12 to 2017/09/03 18:04:57 /* the whole time range */ 2017-09-03 18:06:55,351 DEBUG quick_setup about to run adcpsect as_nav.tmp 2017-09-03 18:06:55,356 INFO quick_run ... ran adcpsect for navsteps 2017-09-03 18:06:55,356 INFO quick_adcp ------------------------- 2017-09-03 18:06:55,356 INFO quick_adcp step 11: nav steps: run refabs 2017-09-03 18:06:55,356 INFO quick_adcp navstep 2 2017-09-03 18:06:55,356 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,356 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/nav 2017-09-03 18:06:55,356 DEBUG quick_setup running python command "refabs" 2017-09-03 18:06:55,356 DEBUG quick_subs fix_file_type: simple reference_file: a_ar.nav fix_file: a_ar.gps output: a_ar.ref year_base= 2017 ensemble_length= 300 gap_tolerance= 10 2017-09-03 18:06:55,356 DEBUG quick_setup about to run refabs refabs.tmp 2017-09-03 18:06:55,360 INFO quick_run ... ran refabs for navsteps 2017-09-03 18:06:55,360 INFO quick_adcp ------------------------- 2017-09-03 18:06:55,360 INFO quick_adcp step 12: nav steps: run smoothr for plots 2017-09-03 18:06:55,360 INFO quick_adcp navstep 3 2017-09-03 18:06:55,360 DEBUG quick_setup nav/smoothr.tmp exists 2017-09-03 18:06:55,360 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,360 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/nav 2017-09-03 18:06:55,360 DEBUG quick_setup running python command "smoothr" 2017-09-03 18:06:55,360 DEBUG quick_subs reference_file: a_ar.nav refabs_output: a_ar.ref output: a_ar.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 2017-09-03 18:06:55,360 DEBUG quick_setup about to run smoothr smoothr.tmp 2017-09-03 18:06:55,369 INFO quick_run ... ran smoothr 2017-09-03 18:06:55,369 INFO quick_adcp ------------------------- 2017-09-03 18:06:55,369 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2017-09-03 18:06:55,369 INFO quick_adcp navstep 4 2017-09-03 18:06:55,369 INFO quick_run smoothing method for ship speed: refsm 2017-09-03 18:06:55,369 INFO quick_run smoothing window: 3 2017-09-03 18:06:55,369 INFO quick_run ship speed source: nav 2017-09-03 18:06:55,369 DEBUG quick_npy Starting: refsm 2017-09-03 18:06:55,383 DEBUG quick_npy Ending: refsm 2017-09-03 18:06:55,383 INFO quick_run ... shipspeed smoothing step done 2017-09-03 18:06:55,383 INFO quick_adcp ------------------------- 2017-09-03 18:06:55,383 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2017-09-03 18:06:55,383 INFO quick_adcp navstep 5 2017-09-03 18:06:55,383 DEBUG quick_setup nav/put_txy.tmp exists 2017-09-03 18:06:55,383 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,383 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/nav 2017-09-03 18:06:55,383 DEBUG quick_setup running python command "put_txy" 2017-09-03 18:06:55,383 DEBUG quick_subs dbname: ../adcpdb/a_ar position_file: a_ar.agt year_base= 2017 tolerance= 5 2017-09-03 18:06:55,383 DEBUG quick_setup about to run put_txy put_txy.tmp 2017-09-03 18:06:55,387 INFO quick_run ... ran put_txy 2017-09-03 18:06:55,387 DEBUG quick_setup nav/put_tuv.tmp exists 2017-09-03 18:06:55,388 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,388 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/nav 2017-09-03 18:06:55,388 DEBUG quick_setup running python command "put_tuv" 2017-09-03 18:06:55,388 DEBUG quick_subs dbname: ../adcpdb/a_ar shipspeed_file: refsm_tuv.asc year_base= 2017 tolerance= 5 2017-09-03 18:06:55,388 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2017-09-03 18:06:55,391 INFO quick_run ... ran put_tuv 2017-09-03 18:06:55,391 DEBUG quick_mpl Starting plot: nav 2017-09-03 18:06:55,563 DEBUG quick_mpl Ending plot: nav 2017-09-03 18:06:55,563 INFO quick_run ... made navigation plot 2017-09-03 18:06:55,563 INFO quick_adcp ------------------------- 2017-09-03 18:06:55,563 INFO quick_adcp step 15: nav steps: make reflayer plots 2017-09-03 18:06:55,563 INFO quick_adcp navstep 6 2017-09-03 18:06:55,563 DEBUG quick_mpl Starting plot: refl 2017-09-03 18:06:55,568 DEBUG quick_mpl found 1.226216 days of data 2017-09-03 18:06:55,568 DEBUG quick_mpl start day is 244.000000 2017-09-03 18:06:55,568 DEBUG quick_mpl figures with 2.000000 days per page 2017-09-03 18:06:55,568 DEBUG quick_mpl printing 1 pages 2017-09-03 18:06:55,568 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2017-09-03 18:06:55,779 DEBUG quick_mpl Ending plot: refl 2017-09-03 18:06:55,779 INFO quick_run ... made reflayer plots 2017-09-03 18:06:55,779 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:55,779 INFO quick_adcp step 10: find profile flags 2017-09-03 18:06:55,779 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,779 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/edit 2017-09-03 18:06:55,779 DEBUG quick_setup running python command "run_autoedit_npy" 2017-09-03 18:06:55,779 DEBUG quick_npy Starting: autoedit 2017-09-03 18:06:55,795 DEBUG pingedit wrote 40 bad bins to abadbin_tmp.asc 2017-09-03 18:06:55,797 DEBUG pingedit wrote 15 bad profiles to abadprf_tmp.asc 2017-09-03 18:06:55,797 DEBUG quick_npy Ending: autoedit 2017-09-03 18:06:55,797 INFO quick_run ... extracted files using automatic editing 2017-09-03 18:06:55,797 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:55,797 INFO quick_adcp step 11: apply editing 2017-09-03 18:06:55,797 DEBUG quick_run starting in: /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,797 DEBUG quick_run executing commands from: edit 2017-09-03 18:06:55,798 DEBUG quick_run about to run dbupdate ../adcpdb/a_ar abadprf_tmp.asc 2017-09-03 18:06:55,801 DEBUG quick_run about to run badbin ../adcpdb/a_ar abadbin_tmp.asc 2017-09-03 18:06:55,804 DEBUG quick_subs dbname: ../adcpdb/a_ar pg_min: 50 set_range_bit time_ranges: all 2017-09-03 18:06:55,804 DEBUG quick_run about to run setflags setflags.tmp 2017-09-03 18:06:55,807 DEBUG quick_run changing directories back to /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,807 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:55,808 INFO quick_adcp step 12: run calibration steps 2017-09-03 18:06:55,808 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2017-09-03 18:06:55,808 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,808 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/cal/botmtrk 2017-09-03 18:06:55,808 DEBUG quick_setup running python command "lst_btrk" 2017-09-03 18:06:55,808 DEBUG quick_subs dbname: ../../adcpdb/a_ar output: a_ar.btm step_size= 1 year_base= 2017 time_ranges: 2017/09/02 12:29:12 to 2017/09/03 18:04:57 /* whole time range */ 2017-09-03 18:06:55,808 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2017-09-03 18:06:55,811 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2017-09-03 18:06:55,811 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,811 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/cal/botmtrk 2017-09-03 18:06:55,811 DEBUG quick_setup running python command "refabsbt" 2017-09-03 18:06:55,811 DEBUG quick_subs fix_file_type: simple reference_file: a_ar.btm fix_file: ../../nav/a_ar.gps output: a_ar.ref year_base= 2017 ensemble_length= 300 gap_tolerance= 60 2017-09-03 18:06:55,811 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2017-09-03 18:06:55,814 INFO quick_run ...bottom track info in check cal/botmtrk 2017-09-03 18:06:55,814 DEBUG quick_mpl Starting plot: btcal 2017-09-03 18:06:55,814 DEBUG quick_mpl No data in a_ar.btm 2017-09-03 18:06:55,814 DEBUG quick_mpl Returning from Btplot with no output 2017-09-03 18:06:55,814 DEBUG quick_mpl Ending plot: btcal 2017-09-03 18:06:55,814 DEBUG quick_setup nav/as_nav.tmp exists 2017-09-03 18:06:55,814 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,814 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/nav 2017-09-03 18:06:55,814 DEBUG quick_setup running python command "as_nav" 2017-09-03 18:06:55,814 DEBUG quick_subs dbname: ../adcpdb/a_ar output: a_ar step_size: 1 ndepth: 20 time_ranges: separate year_base= 2017 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 2017/09/02 12:29:12 to 2017/09/03 18:04:57 /* the whole time range */ 2017-09-03 18:06:55,814 DEBUG quick_setup about to run adcpsect as_nav.tmp 2017-09-03 18:06:55,819 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2017-09-03 18:06:55,819 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:55,819 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/cal/watertrk 2017-09-03 18:06:55,819 DEBUG quick_setup running python command "timslip" 2017-09-03 18:06:55,819 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_ar.gps reference_file: ../../nav/a_ar.nav output_file: a_ar_7.cal year_base= 2017 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 2017-09-03 18:06:55,819 DEBUG quick_setup about to run timslip timslip.tmp 2017-09-03 18:06:55,822 INFO quick_run ... watertrack info in cal/watertrk 2017-09-03 18:06:55,822 DEBUG quick_mpl Starting plot: wtcal 2017-09-03 18:06:55,823 DEBUG quick_mpl Found 15 calibration points 2017-09-03 18:06:56,274 DEBUG quick_mpl Ending plot: wtcal 2017-09-03 18:06:56,274 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:56,275 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/cal/watertrk 2017-09-03 18:06:56,275 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2017-09-03 18:06:56,275 DEBUG quick_npy Starting: guess_xducerxy 2017-09-03 18:06:56,286 DEBUG quick_npy Ending: guess_xducerxy 2017-09-03 18:06:56,286 INFO quick_run ... check cal/watertrk for estimate 2017-09-03 18:06:56,286 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:56,286 INFO quick_adcp step 13: extract and plot temperature 2017-09-03 18:06:56,286 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:56,286 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/edit 2017-09-03 18:06:56,286 DEBUG quick_setup running python command "lst_temp" 2017-09-03 18:06:56,286 DEBUG quick_subs dbname: ../adcpdb/a_ar output: a_ar.tem step_size= 1 year_base= 2017 time_ranges: all 2017-09-03 18:06:56,286 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2017-09-03 18:06:56,290 DEBUG quick_mpl Starting plot: temp 2017-09-03 18:06:56,292 DEBUG quick_mpl plotting 317 points 2017-09-03 18:06:56,414 DEBUG quick_mpl Ending plot: temp 2017-09-03 18:06:56,414 INFO quick_run plotted temperature 2017-09-03 18:06:56,414 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:56,414 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2017-09-03 18:06:56,414 DEBUG quick_setup edit/lst_npings.tmp exists 2017-09-03 18:06:56,414 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:56,414 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/edit 2017-09-03 18:06:56,414 DEBUG quick_setup running python command "lst_npings" 2017-09-03 18:06:56,414 DEBUG quick_subs dbname: ../adcpdb/a_ar output: a_ar_npings.txt step_size= 1 year_base= 2017 time_ranges: all 2017-09-03 18:06:56,414 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2017-09-03 18:06:56,418 DEBUG quick_mpl Starting plot: npings 2017-09-03 18:06:56,420 DEBUG quick_mpl plotting 317 points 2017-09-03 18:06:56,494 DEBUG quick_mpl Ending plot: npings 2017-09-03 18:06:56,494 INFO quick_run ... plotted number of pings per ensemble 2017-09-03 18:06:56,494 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:56,494 INFO quick_adcp step 15: extract matlab "allbins" 2017-09-03 18:06:56,494 DEBUG quick_asect step 18: make matlab files for plotting 2017-09-03 18:06:56,494 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:56,494 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/vector 2017-09-03 18:06:56,494 DEBUG quick_setup running python command "timegrid" 2017-09-03 18:06:56,494 DEBUG quick_setup about to run timegrid a_ar.tmp 2017-09-03 18:06:56,498 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:56,498 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/vector 2017-09-03 18:06:56,498 DEBUG quick_setup running python command "as_vect" 2017-09-03 18:06:56,498 DEBUG quick_setup about to run adcpsect as_vect.tmp 2017-09-03 18:06:56,503 DEBUG quick_asect done making vector matfiles 2017-09-03 18:06:56,503 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:56,503 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/contour 2017-09-03 18:06:56,503 DEBUG quick_setup running python command "timegrid" 2017-09-03 18:06:56,503 DEBUG quick_setup about to run timegrid a_ar.tmp 2017-09-03 18:06:56,506 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:56,506 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/contour 2017-09-03 18:06:56,506 DEBUG quick_setup running python command "as_cont" 2017-09-03 18:06:56,506 DEBUG quick_setup about to run adcpsect as_cont.tmp 2017-09-03 18:06:56,512 DEBUG quick_setup starting in /home/data/AR22/proc/os38nb 2017-09-03 18:06:56,513 DEBUG quick_setup executing commands from /home/data/AR22/proc/os38nb/contour 2017-09-03 18:06:56,513 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_ar 2017-09-03 18:06:56,523 DEBUG quick_asect done running getmat with "allbins" 2017-09-03 18:06:56,524 INFO quick_adcp --------------------------------------------- 2017-09-03 18:06:56,524 INFO quick_adcp writing "cruise_info.txt" 2017-09-03 18:06:56,525 INFO root copying NOFIG to /home/adcp/www/figures/os38nb_hcorr_plot.png 2017-09-03 18:06:56,525 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os38nb_hcorr_plot_thumb.png 2017-09-03 18:06:56,525 DEBUG root matfile is contour/contour_uv.mat 2017-09-03 18:06:56,525 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os38nb_cont_uv.mat 2017-09-03 18:06:56,525 DEBUG root matfile is vector/vector_uv.mat 2017-09-03 18:06:56,525 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os38nb_vect_uv.mat 2017-09-03 18:06:56,525 DEBUG root matfile is contour/contour_xy.mat 2017-09-03 18:06:56,525 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os38nb_cont_xy.mat 2017-09-03 18:06:56,525 DEBUG root matfile is vector/vector_xy.mat 2017-09-03 18:06:56,525 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os38nb_vect_xy.mat 2017-09-03 18:06:56,525 DEBUG root about to copy file edit/a_ar.tem to /home/adcp/www/data/os38nb_temp.asc 2017-09-03 18:06:56,526 INFO root copying edit/a_ar.tem to /home/adcp/www/data/os38nb_temp.asc 2017-09-03 18:06:56,603 DEBUG root about to copy netcdf file /home/data/AR22/proc/os38nb/contour/os38nb.nc to /home/adcp/www/data/os38nb.nc 2017-09-03 18:06:56,604 INFO root copying /home/data/AR22/proc/os38nb/contour/os38nb.nc to /home/adcp/www/data/os38nb.nc 2017-09-03 18:06:56,604 INFO root nc_compressed: ddstep is 1 2017-09-03 18:06:56,629 INFO root success: made compressed nc file /home/adcp/uhdas_tmp/os38nb_compr.nc 2017-09-03 18:06:56,633 INFO root generating pingstats for os38nb 2017-09-03 18:06:56,633 INFO root Ending quick_adcp.py