2016-05-19 19:29:07,713 DEBUG root about to write control file parameters to --yearbase 2016 --cruisename oc1605_transita2 --configtype python --sonar os75nb --dbname a_oc --datatype uhdas --cfgpath /home/data/oc1605_transita2/proc/os75nb/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 1 --xducer_dy -30 ## see config/oc1605_transita2_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 2016-05-19 19:29:07,713 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d os75nb 2016-05-19 19:29:07,715 DEBUG quick_setup found cruise_info.hcorr (ashtech, adu, 3) 2016-05-19 19:29:07,715 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2016-05-19 19:29:07,716 INFO quick_setup fix file is a_oc.gps 2016-05-19 19:29:07,716 INFO quick_setup reflayer: ref_method = refsm 2016-05-19 19:29:07,716 INFO quick_setup reflayer: refuv_source = nav 2016-05-19 19:29:07,716 INFO quick_setup reflayer: refuv_smoothwin = 3 2016-05-19 19:29:07,716 INFO quick_adcp importing numpy version 1.8.2 2016-05-19 19:29:07,732 INFO quick_adcp importing matplotlib version 1.4.3 2016-05-19 19:29:07,968 DEBUG quick_mpl in Q_mpl 2016-05-19 19:29:07,968 INFO quick_adcp ===================================================== 2016-05-19 19:29:07,968 INFO quick_adcp ===================================================== 2016-05-19 19:29:07,968 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d os75nb 2016-05-19 19:29:07,969 INFO quick_adcp cwd is /home/data/oc1605_transita2/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 2016-05-19 19:29:07,969 DEBUG quick_asect extracting matlab files for os75nb 2016-05-19 19:29:07,981 DEBUG quick_setup data directory: /home/data/oc1605_transita2/raw/os75 2016-05-19 19:29:07,982 INFO quick_setup found 108 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/oc1605_transita2/raw/os75/*.raw" 2016-05-19 19:29:07,983 DEBUG quick_setup found 108 files from original filelist 2016-05-19 19:29:07,983 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/oc1605_transita2/raw/os75/oc2016_130_78215.raw ... 2016-05-19 19:29:07,984 DEBUG quick_adcp Thu May 19 19:29:07 2016 running quick_adcp.py as follows: --cntfile /home/data/oc1605_transita2/proc/os75nb/os75nb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_oc 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 28 gridnum 80 increment 10 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/oc1605_transita2/proc/os75nb/config cntfile /home/data/oc1605_transita2/proc/os75nb/os75nb_qpy.cnt commands None configtype python cruisename oc1605_transita2 data_def vmadcp.def datadir /home/data/oc1605_transita2/raw/os75 datafile_glob *.raw datatype uhdas dbname a_oc dday_bailout None debug False ens_len 300 expert None filelist 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'/home/data/oc1605_transita2/raw/os75/oc2016_138_72000.raw', '/home/data/oc1605_transita2/raw/os75/oc2016_138_79200.raw', '/home/data/oc1605_transita2/raw/os75/oc2016_139_00000.raw', '/home/data/oc1605_transita2/raw/os75/oc2016_139_07200.raw', '/home/data/oc1605_transita2/raw/os75/oc2016_139_14400.raw', '/home/data/oc1605_transita2/raw/os75/oc2016_139_21600.raw', '/home/data/oc1605_transita2/raw/os75/oc2016_139_28800.raw', '/home/data/oc1605_transita2/raw/os75/oc2016_139_36000.raw', '/home/data/oc1605_transita2/raw/os75/oc2016_139_43200.raw', '/home/data/oc1605_transita2/raw/os75/oc2016_139_50400.raw', '/home/data/oc1605_transita2/raw/os75/oc2016_139_57600.raw', '/home/data/oc1605_transita2/raw/os75/oc2016_139_64800.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 28 fixfile a_oc.gps fixfilexy a_oc.agt frequency 75 hcorr_inst ashtech 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 2016 py_gbindirbase /home/data/oc1605_transita2/gbin ref_method refsm refuv_inputfile a_oc.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 os75nb steps2rerun sum_xducer_dx 1 sum_xducer_dy -30 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_oc.agt ub_type 1920 uhdas_config yearbase = 2016 uhdas_dir = /home/data/oc1605_transita2 sonar = os75nb gbin = /home/data/oc1605_transita2/gbin gbinsonar = /home/data/oc1605_transita2/gbin/os75 raw = /home/data/oc1605_transita2/raw rawsonar = /home/data/oc1605_transita2/raw/os75 rbin = /home/data/oc1605_transita2/rbin proc = /home/data/oc1605_transita2/proc procsonar = /home/data/oc1605_transita2/proc/os75nb other attributes: gbin_params = hdg_inst : gyro hdg_inst_msgs : [('gyro', 'hdg'), ('ashtech', 'adu')] hdg_msg : hdg pitch_inst : ashtech pitch_msg : adu pos_inst : gpsnav pos_msg : gps roll_inst : ashtech roll_msg : adu hcorr = ['ashtech', 'adu', 3.0] acc_heading_cutoff = 0.02 update_gbin False vardoc False varvals False wtrk_step 7 xducer_dx 1 xducer_dy -30 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 2016-05-19 19:29:07,984 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:07,984 INFO quick_adcp step 1: set up files in "edit" directory 2016-05-19 19:29:07,984 INFO quick_run file exists (edit/clearflags.tmp). not writing 2016-05-19 19:29:07,984 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:07,984 INFO quick_adcp step 2: scan files for time range 2016-05-19 19:29:07,984 DEBUG quick_npy Starting: scanping 2016-05-19 19:29:08,117 DEBUG quick_npy Ending: scanping 2016-05-19 19:29:08,118 DEBUG quick_subs start_end_time 2016/05/10 21:43:38 to 2016/05/10 21:53:52 2016-05-19 19:29:08,118 DEBUG quick_subs dd0: 130.905301 dd1: 130.912407 2016-05-19 19:29:08,118 INFO quick_adcp looking for database with adcpdb/a_oc*.blk 2016-05-19 19:29:08,118 INFO quick_adcp database found: listing blocks 2016-05-19 19:29:08,118 DEBUG quick_subs removing a_ocdir.blk 2016-05-19 19:29:08,119 DEBUG quick_subs about to run mkblkdir 2016-05-19 19:29:08,119 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-05-19 19:29:08,119 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-05-19 19:29:08,133 DEBUG quick_subs database passes. 2016-05-19 19:29:08,133 DEBUG quick_subs start_end_time 2016/05/10 21:48:37 to 2016/05/19 19:13:35 2016-05-19 19:29:08,133 DEBUG quick_subs dd0: 130.908762 dd1: 139.801100 2016-05-19 19:29:08,133 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2016-05-19 19:29:08,134 DEBUG quick_adcp origdb_time_range is 2016/05/10 21:48:37 to 2016/05/19 19:13:35 2016-05-19 19:29:08,134 DEBUG quick_adcp (130.908762 to 139.801100) 2016-05-19 19:29:08,134 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:08,134 INFO quick_adcp step 3: generate averaged data... 2016-05-19 19:29:08,134 INFO quick_run file load/ping_editparams.txt exists. not replacing 2016-05-19 19:29:08,134 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:08,134 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/load 2016-05-19 19:29:08,134 DEBUG quick_setup running python command "run_pingavg_npy" 2016-05-19 19:29:08,134 DEBUG quick_npy Starting: pingavg 2016-05-19 19:29:08,136 DEBUG quick_npy xducerxy is [1, -30] 2016-05-19 19:29:08,137 DEBUG quick_npy singleping editing parameters: 2016-05-19 19:29:08,137 DEBUG quick_npy bigtarget_mab_window : 11 2016-05-19 19:29:08,137 DEBUG quick_npy rl_endbin : 20 2016-05-19 19:29:08,137 DEBUG quick_npy max_search_depth : 2000 2016-05-19 19:29:08,137 DEBUG quick_npy cor_cutoff : 120 2016-05-19 19:29:08,137 DEBUG quick_npy ampfilt : 40 2016-05-19 19:29:08,137 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2016-05-19 19:29:08,137 DEBUG quick_npy rl_startbin : 2 2016-05-19 19:29:08,137 DEBUG quick_npy ecutoff : 0.800000 2016-05-19 19:29:08,137 DEBUG quick_npy refavg_valcutoff : 1 2016-05-19 19:29:08,137 DEBUG quick_npy weakprof_percent : 30 2016-05-19 19:29:08,137 DEBUG quick_npy bigtarget_ampthresh : 55 2016-05-19 19:29:08,143 INFO pingavg ---------------- 2016-05-19 19:29:08,143 INFO pingavg sonar is os75nb 2016-05-19 19:29:08,143 INFO pingavg Pingavg.run for time range 139.750021 to 139.811840 2016-05-19 19:29:08,143 INFO pingavg transducer offset: xducer_dx = 1.000, xducer_dy = -30.000 2016-05-19 19:29:08,143 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2016-05-19 19:29:08,144 INFO pingavg ---------------- 2016-05-19 19:29:08,174 DEBUG pingavg Chunk 1 of 1, 139.750021 to 139.811840 2016-05-19 19:29:08,175 DEBUG pingavg Nothing written 2016-05-19 19:29:08,175 DEBUG quick_npy wrote 0 averages 2016-05-19 19:29:08,175 DEBUG quick_npy Ending: pingavg 2016-05-19 19:29:08,175 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:08,176 INFO quick_adcp step 4: load averaged data (to database) 2016-05-19 19:29:08,176 DEBUG quick_subs in del_overlapping 2016-05-19 19:29:08,176 DEBUG quick_subs lastblock: 2016-05-19 19:29:08,176 DEBUG quick_subs 9 2016-05-19 19:29:08,176 DEBUG quick_subs lastcmd: 2016-05-19 19:29:08,176 DEBUG quick_subs 9 2016-05-19 19:29:08,176 DEBUG quick_subs delblks: 2016-05-19 19:29:08,176 DEBUG quick_subs [9] 2016-05-19 19:29:08,177 DEBUG quick_subs loadblks: 2016-05-19 19:29:08,177 DEBUG quick_subs [9] 2016-05-19 19:29:08,177 DEBUG quick_subs about to run mkblkdir 2016-05-19 19:29:08,177 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-05-19 19:29:08,177 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-05-19 19:29:08,192 DEBUG quick_subs database passes. 2016-05-19 19:29:08,192 DEBUG quick_subs start_end_time 2016/05/10 21:48:37 to 2016/05/19 05:43:36 2016-05-19 19:29:08,192 DEBUG quick_subs dd0: 130.908762 dd1: 139.238611 2016-05-19 19:29:08,192 DEBUG quick_run [9] 2016-05-19 19:29:08,192 DEBUG quick_run cmdlist 2016-05-19 19:29:08,193 DEBUG quick_run ['./ens_blk009.cmd'] 2016-05-19 19:29:08,194 INFO quick_run loaded time range: 2016/05/19 05:48:35 to 2016/05/19 19:28:37 2016-05-19 19:29:08,194 DEBUG quick_setup load/ldcodas.tmp exists 2016-05-19 19:29:08,194 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:08,194 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/load 2016-05-19 19:29:08,194 DEBUG quick_setup running python command "ldcodas" 2016-05-19 19:29:08,195 DEBUG quick_subs filling "thisload" timerange 2016-05-19 19:29:08,196 DEBUG quick_subs in ldcodas 2016-05-19 19:29:08,196 DEBUG quick_subs cmdlist: 2016-05-19 19:29:08,196 DEBUG quick_subs ['./ens_blk009.cmd'] 2016-05-19 19:29:08,196 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_oc DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2016 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk009.cmd 2016-05-19 19:29:08,196 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2016-05-19 19:29:08,228 INFO quick_run 10 block files present 2016-05-19 19:29:08,229 DEBUG quick_subs removing a_ocdir.blk 2016-05-19 19:29:08,229 DEBUG quick_subs about to run mkblkdir 2016-05-19 19:29:08,229 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-05-19 19:29:08,229 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-05-19 19:29:08,243 DEBUG quick_subs database passes. 2016-05-19 19:29:08,244 DEBUG quick_subs start_end_time 2016/05/10 21:48:37 to 2016/05/19 19:28:37 2016-05-19 19:29:08,244 DEBUG quick_subs dd0: 130.908762 dd1: 139.811539 2016-05-19 19:29:08,244 INFO quick_adcp database time range: 2016-05-19 19:29:08,244 INFO quick_adcp 2016/05/10 21:48:37 to 2016/05/19 19:28:37 2016-05-19 19:29:08,244 INFO quick_adcp (130.908762 to 139.811539) 2016-05-19 19:29:08,244 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:08,244 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/adcpdb 2016-05-19 19:29:08,244 DEBUG quick_setup running python command "lst_conf" 2016-05-19 19:29:08,244 DEBUG quick_subs dbname: a_oc output: a_oc.cnh time_ranges: all 2016-05-19 19:29:08,245 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2016-05-19 19:29:08,262 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:08,262 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2016-05-19 19:29:08,262 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2016-05-19 19:29:08,262 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:08,262 INFO quick_adcp step 6: run setflags? 2016-05-19 19:29:08,262 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:08,263 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/edit 2016-05-19 19:29:08,263 DEBUG quick_setup running python command "write_setflags" 2016-05-19 19:29:08,263 DEBUG quick_subs dbname: ../adcpdb/a_oc pg_min: 50 set_range_bit time_ranges: all 2016-05-19 19:29:08,263 DEBUG quick_setup about to run setflags setflags.tmp 2016-05-19 19:29:08,293 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:08,294 INFO quick_adcp step 7: get navigation 2016-05-19 19:29:08,294 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:08,294 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/nav 2016-05-19 19:29:08,294 DEBUG quick_setup running python command "catnav" 2016-05-19 19:29:08,296 INFO quick_subs navigation file nav/a_oc.gps created from load/*.gps2 2016-05-19 19:29:08,297 INFO quick_subs navigation file nav/a_oc.agt created from load/*.gpst2 2016-05-19 19:29:08,299 DEBUG quick_mpl Starting plot: uvship 2016-05-19 19:29:08,802 DEBUG quick_mpl Ending plot: uvship 2016-05-19 19:29:08,802 INFO quick_run plotted uvship 2016-05-19 19:29:08,802 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:08,802 INFO quick_adcp step 8: list heading 2016-05-19 19:29:08,802 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2016-05-19 19:29:08,802 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:08,802 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/cal/rotate 2016-05-19 19:29:08,802 DEBUG quick_setup running python command "lst_hdg" 2016-05-19 19:29:08,802 DEBUG quick_subs dbname: ../../adcpdb/a_oc output: scn.hdg step_size= 1 year_base= 2016 time_ranges: all 2016-05-19 19:29:08,803 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2016-05-19 19:29:08,826 INFO quick_run ... headings extracted 2016-05-19 19:29:08,826 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:08,827 INFO quick_adcp step 9: plot heading correction 2016-05-19 19:29:08,827 DEBUG quick_run hcorr_inst is ashtech 2016-05-19 19:29:08,827 DEBUG quick_mpl Starting plot: hcorr 2016-05-19 19:29:08,855 DEBUG quick_mpl found 8.902782 days of data 2016-05-19 19:29:08,855 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2016-05-19 19:29:08,856 DEBUG quick_mpl printing 3 pages 2016-05-19 19:29:09,701 DEBUG quick_mpl Ending plot: hcorr 2016-05-19 19:29:09,701 INFO quick_run plots are in cal/rotate/*png 2016-05-19 19:29:09,702 INFO quick_adcp ------------------------- 2016-05-19 19:29:09,702 INFO quick_adcp ---- running navsteps --- 2016-05-19 19:29:09,702 INFO quick_adcp ------------------------- 2016-05-19 19:29:09,702 INFO quick_adcp step 10: nav steps: run adcpsect 2016-05-19 19:29:09,702 INFO quick_adcp navstep 1 2016-05-19 19:29:09,702 DEBUG quick_setup nav/as_nav.tmp exists 2016-05-19 19:29:09,702 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:09,702 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/nav 2016-05-19 19:29:09,702 DEBUG quick_setup running python command "as_nav" 2016-05-19 19:29:09,702 DEBUG quick_subs dbname: ../adcpdb/a_oc output: a_oc 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 2016/05/10 21:48:37 to 2016/05/19 19:28:37 /* the whole time range */ 2016-05-19 19:29:09,703 DEBUG quick_setup about to run adcpsect as_nav.tmp 2016-05-19 19:29:09,745 INFO quick_run ... ran adcpsect for navsteps 2016-05-19 19:29:09,745 INFO quick_adcp ------------------------- 2016-05-19 19:29:09,745 INFO quick_adcp step 11: nav steps: run refabs 2016-05-19 19:29:09,745 INFO quick_adcp navstep 2 2016-05-19 19:29:09,746 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:09,746 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/nav 2016-05-19 19:29:09,746 DEBUG quick_setup running python command "refabs" 2016-05-19 19:29:09,746 DEBUG quick_subs fix_file_type: simple reference_file: a_oc.nav fix_file: a_oc.gps output: a_oc.ref year_base= 2016 ensemble_length= 300 gap_tolerance= 10 2016-05-19 19:29:09,746 DEBUG quick_setup about to run refabs refabs.tmp 2016-05-19 19:29:09,778 INFO quick_run ... ran refabs for navsteps 2016-05-19 19:29:09,778 INFO quick_adcp ------------------------- 2016-05-19 19:29:09,778 INFO quick_adcp step 12: nav steps: run smoothr for plots 2016-05-19 19:29:09,779 INFO quick_adcp navstep 3 2016-05-19 19:29:09,779 DEBUG quick_setup nav/smoothr.tmp exists 2016-05-19 19:29:09,779 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:09,779 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/nav 2016-05-19 19:29:09,779 DEBUG quick_setup running python command "smoothr" 2016-05-19 19:29:09,779 DEBUG quick_subs reference_file: a_oc.nav refabs_output: a_oc.ref output: a_oc.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 2016-05-19 19:29:09,779 DEBUG quick_setup about to run smoothr smoothr.tmp 2016-05-19 19:29:09,930 INFO quick_run ... ran smoothr 2016-05-19 19:29:09,930 INFO quick_adcp ------------------------- 2016-05-19 19:29:09,930 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2016-05-19 19:29:09,930 INFO quick_adcp navstep 4 2016-05-19 19:29:09,930 INFO quick_run smoothing method for ship speed: refsm 2016-05-19 19:29:09,930 INFO quick_run smoothing window: 3 2016-05-19 19:29:09,930 INFO quick_run ship speed source: nav 2016-05-19 19:29:09,930 DEBUG quick_npy Starting: refsm 2016-05-19 19:29:10,146 DEBUG quick_npy Ending: refsm 2016-05-19 19:29:10,146 INFO quick_run ... shipspeed smoothing step done 2016-05-19 19:29:10,146 INFO quick_adcp ------------------------- 2016-05-19 19:29:10,146 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2016-05-19 19:29:10,146 INFO quick_adcp navstep 5 2016-05-19 19:29:10,146 DEBUG quick_setup nav/put_txy.tmp exists 2016-05-19 19:29:10,146 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:10,146 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/nav 2016-05-19 19:29:10,147 DEBUG quick_setup running python command "put_txy" 2016-05-19 19:29:10,147 DEBUG quick_subs dbname: ../adcpdb/a_oc position_file: a_oc.agt year_base= 2016 tolerance= 5 2016-05-19 19:29:10,147 DEBUG quick_setup about to run put_txy put_txy.tmp 2016-05-19 19:29:10,184 INFO quick_run ... ran put_txy 2016-05-19 19:29:10,185 DEBUG quick_setup nav/put_tuv.tmp exists 2016-05-19 19:29:10,185 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:10,185 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/nav 2016-05-19 19:29:10,185 DEBUG quick_setup running python command "put_tuv" 2016-05-19 19:29:10,185 DEBUG quick_subs dbname: ../adcpdb/a_oc shipspeed_file: refsm_tuv.asc year_base= 2016 tolerance= 5 2016-05-19 19:29:10,185 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2016-05-19 19:29:10,220 INFO quick_run ... ran put_tuv 2016-05-19 19:29:10,220 DEBUG quick_mpl Starting plot: nav 2016-05-19 19:29:10,640 DEBUG quick_mpl Ending plot: nav 2016-05-19 19:29:10,640 INFO quick_run ... made navigation plot 2016-05-19 19:29:10,640 INFO quick_adcp ------------------------- 2016-05-19 19:29:10,640 INFO quick_adcp step 15: nav steps: make reflayer plots 2016-05-19 19:29:10,641 INFO quick_adcp navstep 6 2016-05-19 19:29:10,641 DEBUG quick_mpl Starting plot: refl 2016-05-19 19:29:10,719 DEBUG quick_mpl found 8.888875 days of data 2016-05-19 19:29:10,719 DEBUG quick_mpl start day is 130.000000 2016-05-19 19:29:10,719 DEBUG quick_mpl figures with 2.000000 days per page 2016-05-19 19:29:10,719 DEBUG quick_mpl printing 5 pages 2016-05-19 19:29:10,719 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2016-05-19 19:29:11,478 DEBUG quick_mpl Ending plot: refl 2016-05-19 19:29:11,478 INFO quick_run ... made reflayer plots 2016-05-19 19:29:11,478 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:11,478 INFO quick_adcp step 10: find profile flags 2016-05-19 19:29:11,478 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:11,478 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/edit 2016-05-19 19:29:11,478 DEBUG quick_setup running python command "run_autoedit_npy" 2016-05-19 19:29:11,478 DEBUG quick_npy Starting: autoedit 2016-05-19 19:29:11,626 DEBUG pingedit wrote 4 bad bins to abadbin_tmp.asc 2016-05-19 19:29:11,644 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2016-05-19 19:29:11,644 DEBUG quick_npy Ending: autoedit 2016-05-19 19:29:11,644 INFO quick_run ... extracted files using automatic editing 2016-05-19 19:29:11,644 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:11,644 INFO quick_adcp step 11: apply editing 2016-05-19 19:29:11,645 DEBUG quick_run starting in: /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:11,645 DEBUG quick_run executing commands from: edit 2016-05-19 19:29:11,646 DEBUG quick_run about to run dbupdate ../adcpdb/a_oc abadprf_tmp.asc 2016-05-19 19:29:11,656 DEBUG quick_run about to run badbin ../adcpdb/a_oc abadbin_tmp.asc 2016-05-19 19:29:11,667 DEBUG quick_subs dbname: ../adcpdb/a_oc pg_min: 50 set_range_bit time_ranges: all 2016-05-19 19:29:11,668 DEBUG quick_run about to run setflags setflags.tmp 2016-05-19 19:29:11,701 DEBUG quick_run changing directories back to /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:11,702 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:11,702 INFO quick_adcp step 12: run calibration steps 2016-05-19 19:29:11,702 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2016-05-19 19:29:11,702 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:11,702 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/cal/botmtrk 2016-05-19 19:29:11,702 DEBUG quick_setup running python command "lst_btrk" 2016-05-19 19:29:11,702 DEBUG quick_subs dbname: ../../adcpdb/a_oc output: a_oc.btm step_size= 1 year_base= 2016 time_ranges: 2016/05/10 21:48:37 to 2016/05/19 19:28:37 /* whole time range */ 2016-05-19 19:29:11,703 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2016-05-19 19:29:11,719 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2016-05-19 19:29:11,720 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:11,720 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/cal/botmtrk 2016-05-19 19:29:11,720 DEBUG quick_setup running python command "refabsbt" 2016-05-19 19:29:11,720 DEBUG quick_subs fix_file_type: simple reference_file: a_oc.btm fix_file: ../../nav/a_oc.gps output: a_oc.ref year_base= 2016 ensemble_length= 300 gap_tolerance= 60 2016-05-19 19:29:11,720 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2016-05-19 19:29:11,729 INFO quick_run ...bottom track info in check cal/botmtrk 2016-05-19 19:29:11,729 DEBUG quick_mpl Starting plot: btcal 2016-05-19 19:29:11,730 DEBUG quick_mpl No data in a_oc.btm 2016-05-19 19:29:11,730 DEBUG quick_mpl Returning from Btplot with no output 2016-05-19 19:29:11,730 DEBUG quick_mpl Ending plot: btcal 2016-05-19 19:29:11,730 DEBUG quick_setup nav/as_nav.tmp exists 2016-05-19 19:29:11,731 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:11,731 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/nav 2016-05-19 19:29:11,731 DEBUG quick_setup running python command "as_nav" 2016-05-19 19:29:11,731 DEBUG quick_subs dbname: ../adcpdb/a_oc output: a_oc 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 2016/05/10 21:48:37 to 2016/05/19 19:28:37 /* the whole time range */ 2016-05-19 19:29:11,731 DEBUG quick_setup about to run adcpsect as_nav.tmp 2016-05-19 19:29:11,777 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2016-05-19 19:29:11,777 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:11,777 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/cal/watertrk 2016-05-19 19:29:11,777 DEBUG quick_setup running python command "timslip" 2016-05-19 19:29:11,777 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_oc.gps reference_file: ../../nav/a_oc.nav output_file: a_oc_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 2016-05-19 19:29:11,777 DEBUG quick_setup about to run timslip timslip.tmp 2016-05-19 19:29:11,796 INFO quick_run ... watertrack info in cal/watertrk 2016-05-19 19:29:11,796 DEBUG quick_mpl Starting plot: wtcal 2016-05-19 19:29:11,798 DEBUG quick_mpl Found 9 calibration points 2016-05-19 19:29:12,814 DEBUG quick_mpl Ending plot: wtcal 2016-05-19 19:29:12,815 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:12,815 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/cal/watertrk 2016-05-19 19:29:12,815 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2016-05-19 19:29:12,815 DEBUG quick_npy Starting: guess_xducerxy 2016-05-19 19:29:12,935 DEBUG quick_npy Ending: guess_xducerxy 2016-05-19 19:29:12,935 INFO quick_run ... check cal/watertrk for estimate 2016-05-19 19:29:12,935 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:12,935 INFO quick_adcp step 13: extract and plot temperature 2016-05-19 19:29:12,936 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:12,936 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/edit 2016-05-19 19:29:12,936 DEBUG quick_setup running python command "lst_temp" 2016-05-19 19:29:12,936 DEBUG quick_subs dbname: ../adcpdb/a_oc output: a_oc.tem step_size= 1 year_base= 2016 time_ranges: all 2016-05-19 19:29:12,936 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2016-05-19 19:29:12,964 DEBUG quick_mpl Starting plot: temp 2016-05-19 19:29:12,991 DEBUG quick_mpl plotting 2565 points 2016-05-19 19:29:13,281 DEBUG quick_mpl Ending plot: temp 2016-05-19 19:29:13,281 INFO quick_run plotted temperature 2016-05-19 19:29:13,282 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:13,282 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2016-05-19 19:29:13,282 DEBUG quick_setup edit/lst_npings.tmp exists 2016-05-19 19:29:13,282 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:13,282 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/edit 2016-05-19 19:29:13,282 DEBUG quick_setup running python command "lst_npings" 2016-05-19 19:29:13,282 DEBUG quick_subs dbname: ../adcpdb/a_oc output: a_oc_npings.txt step_size= 1 year_base= 2016 time_ranges: all 2016-05-19 19:29:13,282 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2016-05-19 19:29:13,310 DEBUG quick_mpl Starting plot: npings 2016-05-19 19:29:13,333 DEBUG quick_mpl plotting 2565 points 2016-05-19 19:29:13,522 DEBUG quick_mpl Ending plot: npings 2016-05-19 19:29:13,522 INFO quick_run ... plotted number of pings per ensemble 2016-05-19 19:29:13,522 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:13,522 INFO quick_adcp step 15: extract matlab "allbins" 2016-05-19 19:29:13,523 DEBUG quick_asect step 18: make matlab files for plotting 2016-05-19 19:29:13,523 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:13,523 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/vector 2016-05-19 19:29:13,523 DEBUG quick_setup running python command "timegrid" 2016-05-19 19:29:13,523 DEBUG quick_setup about to run timegrid a_oc.tmp 2016-05-19 19:29:13,534 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:13,534 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/vector 2016-05-19 19:29:13,534 DEBUG quick_setup running python command "as_vect" 2016-05-19 19:29:13,535 DEBUG quick_setup about to run adcpsect as_vect.tmp 2016-05-19 19:29:13,603 DEBUG quick_asect done making vector matfiles 2016-05-19 19:29:13,603 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:13,603 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/contour 2016-05-19 19:29:13,603 DEBUG quick_setup running python command "timegrid" 2016-05-19 19:29:13,603 DEBUG quick_setup about to run timegrid a_oc.tmp 2016-05-19 19:29:13,614 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:13,614 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/contour 2016-05-19 19:29:13,614 DEBUG quick_setup running python command "as_cont" 2016-05-19 19:29:13,614 DEBUG quick_setup about to run adcpsect as_cont.tmp 2016-05-19 19:29:13,707 DEBUG quick_setup starting in /home/data/oc1605_transita2/proc/os75nb 2016-05-19 19:29:13,707 DEBUG quick_setup executing commands from /home/data/oc1605_transita2/proc/os75nb/contour 2016-05-19 19:29:13,707 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_oc 2016-05-19 19:29:13,945 DEBUG quick_asect done running getmat with "allbins" 2016-05-19 19:29:13,946 INFO quick_adcp --------------------------------------------- 2016-05-19 19:29:13,946 INFO quick_adcp writing "cruise_info.txt" 2016-05-19 19:29:13,948 INFO root copying NOFIG to /home/adcp/www/figures/os75nb_hcorr_plot.png 2016-05-19 19:29:13,948 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os75nb_hcorr_plot_thumb.png 2016-05-19 19:29:13,948 DEBUG root matfile is contour/contour_uv.mat 2016-05-19 19:29:13,952 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os75nb_cont_uv.mat 2016-05-19 19:29:13,952 DEBUG root matfile is vector/vector_uv.mat 2016-05-19 19:29:13,952 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os75nb_vect_uv.mat 2016-05-19 19:29:13,952 DEBUG root matfile is contour/contour_xy.mat 2016-05-19 19:29:13,953 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os75nb_cont_xy.mat 2016-05-19 19:29:13,953 DEBUG root matfile is vector/vector_xy.mat 2016-05-19 19:29:13,953 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os75nb_vect_xy.mat 2016-05-19 19:29:13,953 DEBUG root about to copy file edit/a_oc.tem to /home/adcp/www/data/os75nb_temp.asc 2016-05-19 19:29:13,954 INFO root copying edit/a_oc.tem to /home/adcp/www/data/os75nb_temp.asc 2016-05-19 19:29:13,961 INFO netcdf Using pupynere. 2016-05-19 19:29:14,099 DEBUG root about to copy netcdf file /home/data/oc1605_transita2/proc/os75nb/contour/os75nb.nc to /home/adcp/www/data/os75nb.nc 2016-05-19 19:29:14,151 INFO root copying edit/a_oc.tem to /home/adcp/www/data/os75nb.nc 2016-05-19 19:29:14,195 INFO root generating pingstats for os75nb 2016-05-19 19:29:14,196 INFO root Ending quick_adcp.py