2016-12-06 06:34:04,493 DEBUG root about to write control file parameters to --yearbase 2016 --cruisename EX1608_05 --configtype python --sonar os38bb --dbname a_ex --datatype uhdas --cfgpath /home/data/EX1608_05/proc/os38bb/config --ens_len 300 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea #offset between transducer and gps, applied in at-sea processing # NOTE : read special instructions to change offsets # diagnostics in cal/watertrk/guess_xducerxy.out # parameters used: --xducer_dx 0 --xducer_dy 0 ## see config/EX1608_05_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 2016-12-06 06:34:04,494 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d os38bb 2016-12-06 06:34:04,495 DEBUG quick_setup found cruise_info.hcorr (posmv, pmv, 0) 2016-12-06 06:34:04,496 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2016-12-06 06:34:04,496 INFO quick_setup fix file is a_ex.gps 2016-12-06 06:34:04,496 INFO quick_setup reflayer: ref_method = refsm 2016-12-06 06:34:04,496 INFO quick_setup reflayer: refuv_source = nav 2016-12-06 06:34:04,496 INFO quick_setup reflayer: refuv_smoothwin = 3 2016-12-06 06:34:04,496 INFO quick_adcp importing numpy version 1.8.2 2016-12-06 06:34:04,506 INFO quick_adcp importing matplotlib version 1.4.3 2016-12-06 06:34:04,609 DEBUG quick_mpl in Q_mpl 2016-12-06 06:34:04,609 INFO quick_adcp ===================================================== 2016-12-06 06:34:04,609 INFO quick_adcp ===================================================== 2016-12-06 06:34:04,609 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d os38bb 2016-12-06 06:34:04,609 INFO quick_adcp cwd is /home/data/EX1608_05/proc/os38bb about to run these steps: - write_clearflags - scandata - avg_and_load - codaseditsetup - setflags - getnav - lst_hdg - plot_headcorr - navsteps - find_pflags - apply_edit - navsteps - lst_temp - plot_temp - lst_npings - calib - matfiles - adcpsect - refabs - smoothnav - putnav - refplots - find_pflags - codaseditsetup 2016-12-06 06:34:04,609 DEBUG quick_asect extracting matlab files for os38bb 2016-12-06 06:34:04,610 DEBUG quick_setup data directory: /home/data/EX1608_05/raw/os38 2016-12-06 06:34:04,610 INFO quick_setup found 9 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/EX1608_05/raw/os38/*.raw" 2016-12-06 06:34:04,610 DEBUG quick_setup found 9 files from original filelist 2016-12-06 06:34:04,610 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/EX1608_05/raw/os38/ex2016_339_56032.raw ... 2016-12-06 06:34:04,611 DEBUG quick_adcp Tue Dec 6 06:34:04 2016 running quick_adcp.py as follows: --cntfile /home/data/EX1608_05/proc/os38bb/os38bb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_ex dbpath ../adcpdb deeper_boundaries [100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600] firstdepth 36 gridnum 80 increment 20 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2016 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/EX1608_05/proc/os38bb/config cntfile /home/data/EX1608_05/proc/os38bb/os38bb_qpy.cnt commands None configtype python cruisename EX1608_05 data_def vmadcp.def datadir /home/data/EX1608_05/raw/os38 datafile_glob *.raw datatype uhdas dbname a_ex dday_bailout None debug False ens_len 300 expert None filelist ['/home/data/EX1608_05/raw/os38/ex2016_339_56032.raw', '/home/data/EX1608_05/raw/os38/ex2016_339_57600.raw', '/home/data/EX1608_05/raw/os38/ex2016_339_64800.raw', '/home/data/EX1608_05/raw/os38/ex2016_339_72000.raw', '/home/data/EX1608_05/raw/os38/ex2016_339_79200.raw', '/home/data/EX1608_05/raw/os38/ex2016_340_00000.raw', '/home/data/EX1608_05/raw/os38/ex2016_340_07200.raw', '/home/data/EX1608_05/raw/os38/ex2016_340_14400.raw', '/home/data/EX1608_05/raw/os38/ex2016_340_21600.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 36 fixfile a_ex.gps fixfilexy a_ex.agt frequency 38 hcorr_inst posmv help False incremental True instname os38 jitter 15 max_BLKprofiles 300 max_search_depth 2000 maxrunsecs None min_filter_fraction 0.5 mixed_pings False model os nosave_editcfg 0 numbins 128 pgmin 50 ping_headcorr True pingpref None pingtype bb printformats png proc_engine python proc_yearbase 2016 py_gbindirbase /home/data/EX1608_05/gbin ref_method refsm refuv_inputfile a_ex.gps refuv_smoothwin 3 refuv_source nav rl_endbin 20 rl_startbin 2 rotate_amplitude 1 rotate_angle 0 save_lastens 0 skip_avg True sonar os38bb steps2rerun sum_xducer_dx 0 sum_xducer_dy 0 time_angle_base ens_hcorr time_angle_file ens_hcorr.ang timeout_secs 86400 top_plotbin 1 tuv_file refsm_tuv.asc txy_file a_ex.gps ub_type 1920 uhdas_config yearbase = 2016 uhdas_dir = /home/data/EX1608_05 sonar = os38bb gbin = /home/data/EX1608_05/gbin gbinsonar = /home/data/EX1608_05/gbin/os38 raw = /home/data/EX1608_05/raw rawsonar = /home/data/EX1608_05/raw/os38 rbin = /home/data/EX1608_05/rbin proc = /home/data/EX1608_05/proc procsonar = /home/data/EX1608_05/proc/os38bb other attributes: gbin_params = hdg_inst : gyro hdg_inst_msgs : [('gyro', 'hdg'), ('posmv', 'pmv')] hdg_msg : hdg pitch_inst : posmv pitch_msg : pmv pos_inst : cnav pos_msg : gps roll_inst : posmv roll_msg : pmv hcorr = ['posmv', 'pmv', 0.0] acc_heading_cutoff = 0.02 update_gbin False vardoc False varvals False wtrk_step 7 xducer_dx 0 xducer_dy 0 yearbase 2016 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 2016-12-06 06:34:04,611 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:04,611 INFO quick_adcp step 1: set up files in "edit" directory 2016-12-06 06:34:04,611 INFO quick_run file exists (edit/clearflags.tmp). not writing 2016-12-06 06:34:04,611 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:04,611 INFO quick_adcp step 2: scan files for time range 2016-12-06 06:34:04,611 DEBUG quick_npy Starting: scanping 2016-12-06 06:34:04,617 DEBUG quick_npy Ending: scanping 2016-12-06 06:34:04,618 DEBUG quick_subs start_end_time 2016/12/05 15:33:58 to 2016/12/05 15:44:10 2016-12-06 06:34:04,618 DEBUG quick_subs dd0: 339.648588 dd1: 339.655671 2016-12-06 06:34:04,618 INFO quick_adcp looking for database with adcpdb/a_ex*.blk 2016-12-06 06:34:04,618 INFO quick_adcp database found: listing blocks 2016-12-06 06:34:04,618 DEBUG quick_subs removing a_exdir.blk 2016-12-06 06:34:04,618 DEBUG quick_subs about to run mkblkdir 2016-12-06 06:34:04,618 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-12-06 06:34:04,618 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-12-06 06:34:04,624 DEBUG quick_subs database passes. 2016-12-06 06:34:04,625 DEBUG quick_subs start_end_time 2016/12/05 15:38:52 to 2016/12/06 06:13:55 2016-12-06 06:34:04,625 DEBUG quick_subs dd0: 339.651991 dd1: 340.259664 2016-12-06 06:34:04,625 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2016-12-06 06:34:04,625 DEBUG quick_adcp origdb_time_range is 2016/12/05 15:38:52 to 2016/12/06 06:13:55 2016-12-06 06:34:04,625 DEBUG quick_adcp (339.651991 to 340.259664) 2016-12-06 06:34:04,625 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:04,625 INFO quick_adcp step 3: generate averaged data... 2016-12-06 06:34:04,625 INFO quick_run file load/ping_editparams.txt exists. not replacing 2016-12-06 06:34:04,625 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:04,625 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/load 2016-12-06 06:34:04,625 DEBUG quick_setup running python command "run_pingavg_npy" 2016-12-06 06:34:04,625 DEBUG quick_npy Starting: pingavg 2016-12-06 06:34:04,627 DEBUG quick_npy xducerxy is [0, 0] 2016-12-06 06:34:04,627 DEBUG quick_npy singleping editing parameters: 2016-12-06 06:34:04,627 DEBUG quick_npy bigtarget_mab_window : 11 2016-12-06 06:34:04,627 DEBUG quick_npy rl_endbin : 20 2016-12-06 06:34:04,627 DEBUG quick_npy max_search_depth : 2000 2016-12-06 06:34:04,627 DEBUG quick_npy cor_cutoff : 120 2016-12-06 06:34:04,627 DEBUG quick_npy ampfilt : 40 2016-12-06 06:34:04,627 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2016-12-06 06:34:04,627 DEBUG quick_npy rl_startbin : 2 2016-12-06 06:34:04,627 DEBUG quick_npy ecutoff : 0.800000 2016-12-06 06:34:04,627 DEBUG quick_npy refavg_valcutoff : 1 2016-12-06 06:34:04,627 DEBUG quick_npy weakprof_percent : 30 2016-12-06 06:34:04,627 DEBUG quick_npy bigtarget_ampthresh : 55 2016-12-06 06:34:04,630 INFO pingavg ---------------- 2016-12-06 06:34:04,630 INFO pingavg sonar is os38bb 2016-12-06 06:34:04,630 INFO pingavg Pingavg.run for time range 340.250018 to 340.270225 2016-12-06 06:34:04,630 INFO pingavg transducer offset: xducer_dx = 0.000, xducer_dy = 0.000 2016-12-06 06:34:04,630 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2016-12-06 06:34:04,630 INFO pingavg ---------------- 2016-12-06 06:34:04,645 DEBUG pingavg Chunk 1 of 1, 340.250018 to 340.270225 2016-12-06 06:34:04,645 DEBUG pingavg Nothing written 2016-12-06 06:34:04,645 DEBUG quick_npy wrote 0 averages 2016-12-06 06:34:04,646 DEBUG quick_npy Ending: pingavg 2016-12-06 06:34:04,646 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:04,646 INFO quick_adcp step 4: load averaged data (to database) 2016-12-06 06:34:04,646 DEBUG quick_subs in del_overlapping 2016-12-06 06:34:04,646 DEBUG quick_subs lastblock: 2016-12-06 06:34:04,646 DEBUG quick_subs 1 2016-12-06 06:34:04,646 DEBUG quick_subs lastcmd: 2016-12-06 06:34:04,646 DEBUG quick_subs 1 2016-12-06 06:34:04,646 DEBUG quick_subs delblks: 2016-12-06 06:34:04,646 DEBUG quick_subs [1] 2016-12-06 06:34:04,646 DEBUG quick_subs loadblks: 2016-12-06 06:34:04,646 DEBUG quick_subs [1] 2016-12-06 06:34:04,646 DEBUG quick_run [1] 2016-12-06 06:34:04,646 DEBUG quick_run cmdlist 2016-12-06 06:34:04,646 DEBUG quick_run ['./ens_blk001.cmd'] 2016-12-06 06:34:04,647 DEBUG quick_setup load/ldcodas.tmp exists 2016-12-06 06:34:04,647 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:04,647 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/load 2016-12-06 06:34:04,647 DEBUG quick_setup running python command "ldcodas" 2016-12-06 06:34:04,647 DEBUG quick_subs filling "thisload" timerange 2016-12-06 06:34:04,648 DEBUG quick_subs in ldcodas 2016-12-06 06:34:04,648 DEBUG quick_subs cmdlist: 2016-12-06 06:34:04,648 DEBUG quick_subs ['./ens_blk001.cmd'] 2016-12-06 06:34:04,648 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_ex DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2016 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk001.cmd 2016-12-06 06:34:04,648 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2016-12-06 06:34:04,668 INFO quick_run 2 block files present 2016-12-06 06:34:04,668 DEBUG quick_subs removing a_exdir.blk 2016-12-06 06:34:04,668 DEBUG quick_subs about to run mkblkdir 2016-12-06 06:34:04,668 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-12-06 06:34:04,668 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-12-06 06:34:04,675 DEBUG quick_subs database passes. 2016-12-06 06:34:04,675 DEBUG quick_subs start_end_time 2016/12/05 15:38:52 to 2016/12/06 06:28:55 2016-12-06 06:34:04,675 DEBUG quick_subs dd0: 339.651991 dd1: 340.270081 2016-12-06 06:34:04,675 INFO quick_adcp database time range: 2016-12-06 06:34:04,675 INFO quick_adcp 2016/12/05 15:38:52 to 2016/12/06 06:28:55 2016-12-06 06:34:04,675 INFO quick_adcp (339.651991 to 340.270081) 2016-12-06 06:34:04,675 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:04,675 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/adcpdb 2016-12-06 06:34:04,676 DEBUG quick_setup running python command "lst_conf" 2016-12-06 06:34:04,676 DEBUG quick_subs dbname: a_ex output: a_ex.cnh time_ranges: all 2016-12-06 06:34:04,676 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2016-12-06 06:34:04,680 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:04,680 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2016-12-06 06:34:04,680 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2016-12-06 06:34:04,680 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:04,680 INFO quick_adcp step 6: run setflags? 2016-12-06 06:34:04,680 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:04,680 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/edit 2016-12-06 06:34:04,680 DEBUG quick_setup running python command "write_setflags" 2016-12-06 06:34:04,680 DEBUG quick_subs dbname: ../adcpdb/a_ex pg_min: 50 set_range_bit time_ranges: all 2016-12-06 06:34:04,681 DEBUG quick_setup about to run setflags setflags.tmp 2016-12-06 06:34:04,686 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:04,686 INFO quick_adcp step 7: get navigation 2016-12-06 06:34:04,686 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:04,686 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/nav 2016-12-06 06:34:04,686 DEBUG quick_setup running python command "catnav" 2016-12-06 06:34:04,686 INFO quick_subs navigation file nav/a_ex.gps created from load/*.gps2 2016-12-06 06:34:04,687 INFO quick_subs navigation file nav/a_ex.agt created from load/*.gpst2 2016-12-06 06:34:04,687 DEBUG quick_mpl Starting plot: uvship 2016-12-06 06:34:04,911 DEBUG quick_mpl Ending plot: uvship 2016-12-06 06:34:04,911 INFO quick_run plotted uvship 2016-12-06 06:34:04,911 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:04,911 INFO quick_adcp step 8: list heading 2016-12-06 06:34:04,911 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2016-12-06 06:34:04,911 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:04,911 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/cal/rotate 2016-12-06 06:34:04,911 DEBUG quick_setup running python command "lst_hdg" 2016-12-06 06:34:04,911 DEBUG quick_subs dbname: ../../adcpdb/a_ex output: scn.hdg step_size= 1 year_base= 2016 time_ranges: all 2016-12-06 06:34:04,911 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2016-12-06 06:34:04,915 INFO quick_run ... headings extracted 2016-12-06 06:34:04,916 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:04,916 INFO quick_adcp step 9: plot heading correction 2016-12-06 06:34:04,916 DEBUG quick_run hcorr_inst is posmv 2016-12-06 06:34:04,916 DEBUG quick_mpl Starting plot: hcorr 2016-12-06 06:34:04,917 DEBUG quick_mpl found 0.618093 days of data 2016-12-06 06:34:04,917 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2016-12-06 06:34:04,917 DEBUG quick_mpl printing 1 pages 2016-12-06 06:34:05,121 DEBUG quick_mpl Ending plot: hcorr 2016-12-06 06:34:05,122 INFO quick_run plots are in cal/rotate/*png 2016-12-06 06:34:05,122 INFO quick_adcp ------------------------- 2016-12-06 06:34:05,122 INFO quick_adcp ---- running navsteps --- 2016-12-06 06:34:05,122 INFO quick_adcp ------------------------- 2016-12-06 06:34:05,122 INFO quick_adcp step 10: nav steps: run adcpsect 2016-12-06 06:34:05,122 INFO quick_adcp navstep 1 2016-12-06 06:34:05,122 DEBUG quick_setup nav/as_nav.tmp exists 2016-12-06 06:34:05,122 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,122 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/nav 2016-12-06 06:34:05,122 DEBUG quick_setup running python command "as_nav" 2016-12-06 06:34:05,122 DEBUG quick_subs dbname: ../adcpdb/a_ex output: a_ex step_size: 1 ndepth: 20 time_ranges: separate year_base= 2016 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 2016/12/05 15:38:52 to 2016/12/06 06:28:55 /* the whole time range */ 2016-12-06 06:34:05,122 DEBUG quick_setup about to run adcpsect as_nav.tmp 2016-12-06 06:34:05,129 INFO quick_run ... ran adcpsect for navsteps 2016-12-06 06:34:05,129 INFO quick_adcp ------------------------- 2016-12-06 06:34:05,129 INFO quick_adcp step 11: nav steps: run refabs 2016-12-06 06:34:05,129 INFO quick_adcp navstep 2 2016-12-06 06:34:05,129 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,129 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/nav 2016-12-06 06:34:05,129 DEBUG quick_setup running python command "refabs" 2016-12-06 06:34:05,129 DEBUG quick_subs fix_file_type: simple reference_file: a_ex.nav fix_file: a_ex.gps output: a_ex.ref year_base= 2016 ensemble_length= 300 gap_tolerance= 10 2016-12-06 06:34:05,129 DEBUG quick_setup about to run refabs refabs.tmp 2016-12-06 06:34:05,134 INFO quick_run ... ran refabs for navsteps 2016-12-06 06:34:05,134 INFO quick_adcp ------------------------- 2016-12-06 06:34:05,135 INFO quick_adcp step 12: nav steps: run smoothr for plots 2016-12-06 06:34:05,135 INFO quick_adcp navstep 3 2016-12-06 06:34:05,135 DEBUG quick_setup nav/smoothr.tmp exists 2016-12-06 06:34:05,135 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,135 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/nav 2016-12-06 06:34:05,135 DEBUG quick_setup running python command "smoothr" 2016-12-06 06:34:05,135 DEBUG quick_subs reference_file: a_ex.nav refabs_output: a_ex.ref output: a_ex.sm filter_hwidth= 0.0208 min_filter_fraction= 0.5 max_gap_ratio= 0.05 max_gap_distance= 50 max_gap_time= 30 /* 0.5 minutes */ ensemble_time= 300 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2016-12-06 06:34:05,135 DEBUG quick_setup about to run smoothr smoothr.tmp 2016-12-06 06:34:05,155 INFO quick_run ... ran smoothr 2016-12-06 06:34:05,155 INFO quick_adcp ------------------------- 2016-12-06 06:34:05,155 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2016-12-06 06:34:05,155 INFO quick_adcp navstep 4 2016-12-06 06:34:05,155 INFO quick_run smoothing method for ship speed: refsm 2016-12-06 06:34:05,155 INFO quick_run smoothing window: 3 2016-12-06 06:34:05,156 INFO quick_run ship speed source: nav 2016-12-06 06:34:05,156 DEBUG quick_npy Starting: refsm 2016-12-06 06:34:05,169 DEBUG quick_npy Ending: refsm 2016-12-06 06:34:05,169 INFO quick_run ... shipspeed smoothing step done 2016-12-06 06:34:05,169 INFO quick_adcp ------------------------- 2016-12-06 06:34:05,169 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2016-12-06 06:34:05,169 INFO quick_adcp navstep 5 2016-12-06 06:34:05,169 DEBUG quick_setup nav/put_txy.tmp exists 2016-12-06 06:34:05,169 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,169 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/nav 2016-12-06 06:34:05,169 DEBUG quick_setup running python command "put_txy" 2016-12-06 06:34:05,169 DEBUG quick_subs dbname: ../adcpdb/a_ex position_file: a_ex.gps year_base= 2016 tolerance= 5 2016-12-06 06:34:05,169 DEBUG quick_setup about to run put_txy put_txy.tmp 2016-12-06 06:34:05,174 INFO quick_run ... ran put_txy 2016-12-06 06:34:05,174 DEBUG quick_setup nav/put_tuv.tmp exists 2016-12-06 06:34:05,174 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,174 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/nav 2016-12-06 06:34:05,174 DEBUG quick_setup running python command "put_tuv" 2016-12-06 06:34:05,174 DEBUG quick_subs dbname: ../adcpdb/a_ex shipspeed_file: refsm_tuv.asc year_base= 2016 tolerance= 5 2016-12-06 06:34:05,174 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2016-12-06 06:34:05,178 INFO quick_run ... ran put_tuv 2016-12-06 06:34:05,179 DEBUG quick_mpl Starting plot: nav 2016-12-06 06:34:05,370 DEBUG quick_mpl Ending plot: nav 2016-12-06 06:34:05,370 INFO quick_run ... made navigation plot 2016-12-06 06:34:05,370 INFO quick_adcp ------------------------- 2016-12-06 06:34:05,370 INFO quick_adcp step 15: nav steps: make reflayer plots 2016-12-06 06:34:05,370 INFO quick_adcp navstep 6 2016-12-06 06:34:05,371 DEBUG quick_mpl Starting plot: refl 2016-12-06 06:34:05,373 DEBUG quick_mpl found 0.611149 days of data 2016-12-06 06:34:05,374 DEBUG quick_mpl start day is 339.000000 2016-12-06 06:34:05,374 DEBUG quick_mpl figures with 2.000000 days per page 2016-12-06 06:34:05,374 DEBUG quick_mpl printing 1 pages 2016-12-06 06:34:05,374 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2016-12-06 06:34:05,567 DEBUG quick_mpl Ending plot: refl 2016-12-06 06:34:05,567 INFO quick_run ... made reflayer plots 2016-12-06 06:34:05,567 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:05,567 INFO quick_adcp step 10: find profile flags 2016-12-06 06:34:05,567 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,567 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/edit 2016-12-06 06:34:05,567 DEBUG quick_setup running python command "run_autoedit_npy" 2016-12-06 06:34:05,567 DEBUG quick_npy Starting: autoedit 2016-12-06 06:34:05,581 DEBUG pingedit wrote 2 bad bins to abadbin_tmp.asc 2016-12-06 06:34:05,583 DEBUG pingedit wrote 2 bad profiles to abadprf_tmp.asc 2016-12-06 06:34:05,583 DEBUG quick_npy Ending: autoedit 2016-12-06 06:34:05,583 INFO quick_run ... extracted files using automatic editing 2016-12-06 06:34:05,583 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:05,583 INFO quick_adcp step 11: apply editing 2016-12-06 06:34:05,583 DEBUG quick_run starting in: /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,583 DEBUG quick_run executing commands from: edit 2016-12-06 06:34:05,584 DEBUG quick_run about to run dbupdate ../adcpdb/a_ex abadprf_tmp.asc 2016-12-06 06:34:05,588 DEBUG quick_run about to run badbin ../adcpdb/a_ex abadbin_tmp.asc 2016-12-06 06:34:05,592 DEBUG quick_subs dbname: ../adcpdb/a_ex pg_min: 50 set_range_bit time_ranges: all 2016-12-06 06:34:05,592 DEBUG quick_run about to run setflags setflags.tmp 2016-12-06 06:34:05,601 DEBUG quick_run changing directories back to /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,601 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:05,601 INFO quick_adcp step 12: run calibration steps 2016-12-06 06:34:05,601 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2016-12-06 06:34:05,601 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,602 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/cal/botmtrk 2016-12-06 06:34:05,602 DEBUG quick_setup running python command "lst_btrk" 2016-12-06 06:34:05,602 DEBUG quick_subs dbname: ../../adcpdb/a_ex output: a_ex.btm step_size= 1 year_base= 2016 time_ranges: 2016/12/05 15:38:52 to 2016/12/06 06:28:55 /* whole time range */ 2016-12-06 06:34:05,602 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2016-12-06 06:34:05,608 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2016-12-06 06:34:05,609 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,609 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/cal/botmtrk 2016-12-06 06:34:05,609 DEBUG quick_setup running python command "refabsbt" 2016-12-06 06:34:05,609 DEBUG quick_subs fix_file_type: simple reference_file: a_ex.btm fix_file: ../../nav/a_ex.gps output: a_ex.ref year_base= 2016 ensemble_length= 300 gap_tolerance= 60 2016-12-06 06:34:05,609 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2016-12-06 06:34:05,614 INFO quick_run ...bottom track info in check cal/botmtrk 2016-12-06 06:34:05,614 DEBUG quick_mpl Starting plot: btcal 2016-12-06 06:34:05,615 DEBUG quick_mpl No data in a_ex.btm 2016-12-06 06:34:05,615 DEBUG quick_mpl Returning from Btplot with no output 2016-12-06 06:34:05,615 DEBUG quick_mpl Ending plot: btcal 2016-12-06 06:34:05,615 DEBUG quick_setup nav/as_nav.tmp exists 2016-12-06 06:34:05,615 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,615 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/nav 2016-12-06 06:34:05,615 DEBUG quick_setup running python command "as_nav" 2016-12-06 06:34:05,615 DEBUG quick_subs dbname: ../adcpdb/a_ex output: a_ex step_size: 1 ndepth: 20 time_ranges: separate year_base= 2016 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 2016/12/05 15:38:52 to 2016/12/06 06:28:55 /* the whole time range */ 2016-12-06 06:34:05,615 DEBUG quick_setup about to run adcpsect as_nav.tmp 2016-12-06 06:34:05,623 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2016-12-06 06:34:05,623 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:05,623 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/cal/watertrk 2016-12-06 06:34:05,623 DEBUG quick_setup running python command "timslip" 2016-12-06 06:34:05,623 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_ex.gps reference_file: ../../nav/a_ex.nav output_file: a_ex_7.cal year_base= 2016 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 2016-12-06 06:34:05,623 DEBUG quick_setup about to run timslip timslip.tmp 2016-12-06 06:34:05,629 INFO quick_run ... watertrack info in cal/watertrk 2016-12-06 06:34:05,629 DEBUG quick_mpl Starting plot: wtcal 2016-12-06 06:34:05,630 DEBUG quick_mpl Found 2 calibration points 2016-12-06 06:34:06,161 DEBUG quick_mpl Ending plot: wtcal 2016-12-06 06:34:06,161 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:06,161 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/cal/watertrk 2016-12-06 06:34:06,162 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2016-12-06 06:34:06,162 DEBUG quick_npy Starting: guess_xducerxy 2016-12-06 06:34:06,172 DEBUG quick_npy Ending: guess_xducerxy 2016-12-06 06:34:06,172 INFO quick_run ... check cal/watertrk for estimate 2016-12-06 06:34:06,172 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:06,172 INFO quick_adcp step 13: extract and plot temperature 2016-12-06 06:34:06,173 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:06,173 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/edit 2016-12-06 06:34:06,173 DEBUG quick_setup running python command "lst_temp" 2016-12-06 06:34:06,173 DEBUG quick_subs dbname: ../adcpdb/a_ex output: a_ex.tem step_size= 1 year_base= 2016 time_ranges: all 2016-12-06 06:34:06,173 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2016-12-06 06:34:06,178 DEBUG quick_mpl Starting plot: temp 2016-12-06 06:34:06,179 DEBUG quick_mpl plotting 179 points 2016-12-06 06:34:06,319 DEBUG quick_mpl Ending plot: temp 2016-12-06 06:34:06,319 INFO quick_run plotted temperature 2016-12-06 06:34:06,320 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:06,320 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2016-12-06 06:34:06,320 DEBUG quick_setup edit/lst_npings.tmp exists 2016-12-06 06:34:06,320 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:06,320 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/edit 2016-12-06 06:34:06,320 DEBUG quick_setup running python command "lst_npings" 2016-12-06 06:34:06,320 DEBUG quick_subs dbname: ../adcpdb/a_ex output: a_ex_npings.txt step_size= 1 year_base= 2016 time_ranges: all 2016-12-06 06:34:06,320 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2016-12-06 06:34:06,325 DEBUG quick_mpl Starting plot: npings 2016-12-06 06:34:06,326 DEBUG quick_mpl plotting 179 points 2016-12-06 06:34:06,419 DEBUG quick_mpl Ending plot: npings 2016-12-06 06:34:06,419 INFO quick_run ... plotted number of pings per ensemble 2016-12-06 06:34:06,419 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:06,419 INFO quick_adcp step 15: extract matlab "allbins" 2016-12-06 06:34:06,419 DEBUG quick_asect step 18: make matlab files for plotting 2016-12-06 06:34:06,419 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:06,419 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/vector 2016-12-06 06:34:06,419 DEBUG quick_setup running python command "timegrid" 2016-12-06 06:34:06,419 DEBUG quick_setup about to run timegrid a_ex.tmp 2016-12-06 06:34:06,423 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:06,423 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/vector 2016-12-06 06:34:06,424 DEBUG quick_setup running python command "as_vect" 2016-12-06 06:34:06,424 DEBUG quick_setup about to run adcpsect as_vect.tmp 2016-12-06 06:34:06,430 DEBUG quick_asect done making vector matfiles 2016-12-06 06:34:06,430 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:06,430 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/contour 2016-12-06 06:34:06,430 DEBUG quick_setup running python command "timegrid" 2016-12-06 06:34:06,430 DEBUG quick_setup about to run timegrid a_ex.tmp 2016-12-06 06:34:06,436 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:06,436 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/contour 2016-12-06 06:34:06,436 DEBUG quick_setup running python command "as_cont" 2016-12-06 06:34:06,436 DEBUG quick_setup about to run adcpsect as_cont.tmp 2016-12-06 06:34:06,450 DEBUG quick_setup starting in /home/data/EX1608_05/proc/os38bb 2016-12-06 06:34:06,450 DEBUG quick_setup executing commands from /home/data/EX1608_05/proc/os38bb/contour 2016-12-06 06:34:06,450 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_ex 2016-12-06 06:34:06,465 DEBUG quick_asect done running getmat with "allbins" 2016-12-06 06:34:06,465 INFO quick_adcp --------------------------------------------- 2016-12-06 06:34:06,465 INFO quick_adcp writing "cruise_info.txt" 2016-12-06 06:34:06,466 INFO root copying NOFIG to /home/adcp/www/figures/os38bb_hcorr_plot.png 2016-12-06 06:34:06,466 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os38bb_hcorr_plot_thumb.png 2016-12-06 06:34:06,466 DEBUG root matfile is contour/contour_uv.mat 2016-12-06 06:34:06,467 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os38bb_cont_uv.mat 2016-12-06 06:34:06,467 DEBUG root matfile is vector/vector_uv.mat 2016-12-06 06:34:06,467 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os38bb_vect_uv.mat 2016-12-06 06:34:06,467 DEBUG root matfile is contour/contour_xy.mat 2016-12-06 06:34:06,467 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os38bb_cont_xy.mat 2016-12-06 06:34:06,467 DEBUG root matfile is vector/vector_xy.mat 2016-12-06 06:34:06,467 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os38bb_vect_xy.mat 2016-12-06 06:34:06,467 DEBUG root about to copy file edit/a_ex.tem to /home/adcp/www/data/os38bb_temp.asc 2016-12-06 06:34:06,467 INFO root copying edit/a_ex.tem to /home/adcp/www/data/os38bb_temp.asc 2016-12-06 06:34:06,480 INFO netcdf Using scipy. 2016-12-06 06:34:06,490 DEBUG root about to copy netcdf file /home/data/EX1608_05/proc/os38bb/contour/os38bb.nc to /home/adcp/www/data/os38bb.nc 2016-12-06 06:34:06,490 INFO root copying edit/a_ex.tem to /home/adcp/www/data/os38bb.nc 2016-12-06 06:34:06,495 INFO root generating pingstats for os38bb 2016-12-06 06:34:06,495 INFO root Ending quick_adcp.py