2016-08-07 10:59:31,149 DEBUG root about to write control file parameters to --yearbase 2016 --cruisename AT36 --configtype python --sonar wh300 --dbname a_at --datatype uhdas --cfgpath /home/data/AT36/proc/wh300/config --ens_len 120 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea # xducer_dx, xducer_dy not set ## see config/AT36_proc.py for other settings --skip_avg ## see above --max_search_depth 500 --ping_headcorr --proc_engine python --refuv_smoothwin 3 --incremental --find_pflags --top_plotbin 1 --auto 2016-08-07 10:59:31,149 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d wh300 2016-08-07 10:59:31,150 DEBUG quick_setup found cruise_info.hcorr (phins, hdg, 0) 2016-08-07 10:59:31,150 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2016-08-07 10:59:31,151 INFO quick_setup fix file is a_at.gps 2016-08-07 10:59:31,151 INFO quick_setup reflayer: ref_method = refsm 2016-08-07 10:59:31,151 INFO quick_setup reflayer: refuv_source = nav 2016-08-07 10:59:31,151 INFO quick_setup reflayer: refuv_smoothwin = 3 2016-08-07 10:59:31,151 INFO quick_adcp importing numpy version 1.8.2 2016-08-07 10:59:31,159 INFO quick_adcp importing matplotlib version 1.4.3 2016-08-07 10:59:31,245 DEBUG quick_mpl in Q_mpl 2016-08-07 10:59:31,245 INFO quick_adcp ===================================================== 2016-08-07 10:59:31,245 INFO quick_adcp ===================================================== 2016-08-07 10:59:31,245 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d wh300 2016-08-07 10:59:31,245 INFO quick_adcp cwd is /home/data/AT36/proc/wh300 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 2016-08-07 10:59:31,246 DEBUG quick_asect extracting matlab files for wh300 2016-08-07 10:59:31,252 DEBUG quick_setup data directory: /home/data/AT36/raw/wh300 2016-08-07 10:59:31,252 INFO quick_setup found 112 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/AT36/raw/wh300/*.raw" 2016-08-07 10:59:31,252 DEBUG quick_setup found 112 files from original filelist 2016-08-07 10:59:31,252 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/AT36/raw/wh300/at2016_209_57463.raw ... 2016-08-07 10:59:31,253 DEBUG quick_adcp Sun Aug 7 10:59:31 2016 running quick_adcp.py as follows: --cntfile /home/data/AT36/proc/wh300/wh300_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_at dbpath ../adcpdb deeper_boundaries [40, 60, 80, 100, 120] firstdepth 13 gridnum 80 increment 2 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 20 bl_half_width 3 btrk_step 1.5 cfgpath /home/data/AT36/proc/wh300/config cntfile /home/data/AT36/proc/wh300/wh300_qpy.cnt commands None configtype python cruisename AT36 data_def vmadcp.def datadir /home/data/AT36/raw/wh300 datafile_glob *.raw datatype uhdas dbname a_at dday_bailout None debug False ens_len 120 expert None filelist ['/home/data/AT36/raw/wh300/at2016_209_57463.raw', '/home/data/AT36/raw/wh300/at2016_209_57600.raw', '/home/data/AT36/raw/wh300/at2016_209_62071.raw', '/home/data/AT36/raw/wh300/at2016_209_64800.raw', '/home/data/AT36/raw/wh300/at2016_209_65787.raw', '/home/data/AT36/raw/wh300/at2016_209_72000.raw', '/home/data/AT36/raw/wh300/at2016_209_79200.raw', '/home/data/AT36/raw/wh300/at2016_210_00000.raw', '/home/data/AT36/raw/wh300/at2016_210_07200.raw', '/home/data/AT36/raw/wh300/at2016_210_14400.raw', '/home/data/AT36/raw/wh300/at2016_210_21600.raw', '/home/data/AT36/raw/wh300/at2016_210_28800.raw', '/home/data/AT36/raw/wh300/at2016_210_36000.raw', '/home/data/AT36/raw/wh300/at2016_210_43200.raw', '/home/data/AT36/raw/wh300/at2016_210_50400.raw', '/home/data/AT36/raw/wh300/at2016_211_39606.raw', '/home/data/AT36/raw/wh300/at2016_211_43200.raw', '/home/data/AT36/raw/wh300/at2016_211_50400.raw', '/home/data/AT36/raw/wh300/at2016_211_57600.raw', '/home/data/AT36/raw/wh300/at2016_211_64800.raw', '/home/data/AT36/raw/wh300/at2016_211_72000.raw', '/home/data/AT36/raw/wh300/at2016_211_79200.raw', '/home/data/AT36/raw/wh300/at2016_212_00000.raw', '/home/data/AT36/raw/wh300/at2016_212_07200.raw', '/home/data/AT36/raw/wh300/at2016_212_14400.raw', '/home/data/AT36/raw/wh300/at2016_212_21600.raw', '/home/data/AT36/raw/wh300/at2016_212_28800.raw', '/home/data/AT36/raw/wh300/at2016_212_36000.raw', '/home/data/AT36/raw/wh300/at2016_212_43200.raw', '/home/data/AT36/raw/wh300/at2016_212_50400.raw', '/home/data/AT36/raw/wh300/at2016_212_57600.raw', '/home/data/AT36/raw/wh300/at2016_212_64800.raw', '/home/data/AT36/raw/wh300/at2016_212_72000.raw', '/home/data/AT36/raw/wh300/at2016_212_79200.raw', '/home/data/AT36/raw/wh300/at2016_213_00000.raw', '/home/data/AT36/raw/wh300/at2016_213_07200.raw', '/home/data/AT36/raw/wh300/at2016_213_14400.raw', '/home/data/AT36/raw/wh300/at2016_213_21600.raw', '/home/data/AT36/raw/wh300/at2016_213_28800.raw', '/home/data/AT36/raw/wh300/at2016_213_36000.raw', '/home/data/AT36/raw/wh300/at2016_213_43200.raw', '/home/data/AT36/raw/wh300/at2016_213_50400.raw', '/home/data/AT36/raw/wh300/at2016_213_57600.raw', '/home/data/AT36/raw/wh300/at2016_213_64800.raw', '/home/data/AT36/raw/wh300/at2016_213_72000.raw', '/home/data/AT36/raw/wh300/at2016_213_79200.raw', '/home/data/AT36/raw/wh300/at2016_214_00000.raw', '/home/data/AT36/raw/wh300/at2016_214_07200.raw', '/home/data/AT36/raw/wh300/at2016_214_14400.raw', '/home/data/AT36/raw/wh300/at2016_214_21600.raw', '/home/data/AT36/raw/wh300/at2016_214_28800.raw', '/home/data/AT36/raw/wh300/at2016_214_36000.raw', '/home/data/AT36/raw/wh300/at2016_214_40456.raw', '/home/data/AT36/raw/wh300/at2016_214_43200.raw', '/home/data/AT36/raw/wh300/at2016_214_50400.raw', '/home/data/AT36/raw/wh300/at2016_214_72681.raw', '/home/data/AT36/raw/wh300/at2016_214_79200.raw', '/home/data/AT36/raw/wh300/at2016_214_84566.raw', '/home/data/AT36/raw/wh300/at2016_215_00000.raw', '/home/data/AT36/raw/wh300/at2016_215_07200.raw', '/home/data/AT36/raw/wh300/at2016_215_14400.raw', '/home/data/AT36/raw/wh300/at2016_215_21600.raw', '/home/data/AT36/raw/wh300/at2016_215_28800.raw', '/home/data/AT36/raw/wh300/at2016_215_36000.raw', '/home/data/AT36/raw/wh300/at2016_215_43200.raw', '/home/data/AT36/raw/wh300/at2016_215_50400.raw', '/home/data/AT36/raw/wh300/at2016_215_57600.raw', '/home/data/AT36/raw/wh300/at2016_215_64800.raw', '/home/data/AT36/raw/wh300/at2016_215_72000.raw', '/home/data/AT36/raw/wh300/at2016_215_79200.raw', '/home/data/AT36/raw/wh300/at2016_216_00000.raw', '/home/data/AT36/raw/wh300/at2016_216_07200.raw', '/home/data/AT36/raw/wh300/at2016_216_14400.raw', '/home/data/AT36/raw/wh300/at2016_216_21600.raw', '/home/data/AT36/raw/wh300/at2016_216_28800.raw', '/home/data/AT36/raw/wh300/at2016_216_36000.raw', '/home/data/AT36/raw/wh300/at2016_216_43200.raw', '/home/data/AT36/raw/wh300/at2016_216_50400.raw', '/home/data/AT36/raw/wh300/at2016_216_57600.raw', '/home/data/AT36/raw/wh300/at2016_216_64800.raw', '/home/data/AT36/raw/wh300/at2016_216_72000.raw', '/home/data/AT36/raw/wh300/at2016_216_79200.raw', '/home/data/AT36/raw/wh300/at2016_217_00000.raw', '/home/data/AT36/raw/wh300/at2016_217_07200.raw', '/home/data/AT36/raw/wh300/at2016_217_14400.raw', '/home/data/AT36/raw/wh300/at2016_217_21600.raw', '/home/data/AT36/raw/wh300/at2016_217_28800.raw', '/home/data/AT36/raw/wh300/at2016_217_36000.raw', '/home/data/AT36/raw/wh300/at2016_217_43200.raw', '/home/data/AT36/raw/wh300/at2016_217_50400.raw', '/home/data/AT36/raw/wh300/at2016_217_57600.raw', '/home/data/AT36/raw/wh300/at2016_217_64800.raw', '/home/data/AT36/raw/wh300/at2016_217_72000.raw', '/home/data/AT36/raw/wh300/at2016_217_79200.raw', '/home/data/AT36/raw/wh300/at2016_218_00000.raw', '/home/data/AT36/raw/wh300/at2016_218_07200.raw', '/home/data/AT36/raw/wh300/at2016_218_14400.raw', '/home/data/AT36/raw/wh300/at2016_218_21600.raw', '/home/data/AT36/raw/wh300/at2016_218_28800.raw', '/home/data/AT36/raw/wh300/at2016_218_36000.raw', '/home/data/AT36/raw/wh300/at2016_218_43200.raw', '/home/data/AT36/raw/wh300/at2016_218_50400.raw', '/home/data/AT36/raw/wh300/at2016_218_57600.raw', '/home/data/AT36/raw/wh300/at2016_218_64800.raw', '/home/data/AT36/raw/wh300/at2016_218_72000.raw', '/home/data/AT36/raw/wh300/at2016_218_79200.raw', '/home/data/AT36/raw/wh300/at2016_219_00000.raw', '/home/data/AT36/raw/wh300/at2016_219_07200.raw', '/home/data/AT36/raw/wh300/at2016_219_14400.raw', '/home/data/AT36/raw/wh300/at2016_219_21600.raw', '/home/data/AT36/raw/wh300/at2016_219_28800.raw', '/home/data/AT36/raw/wh300/at2016_219_36000.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 13 fixfile a_at.gps fixfilexy a_at.agt frequency 300 hcorr_inst phins help False incremental True instname wh300 jitter 15 max_BLKprofiles 300 max_search_depth 500 maxrunsecs None min_filter_fraction 0.5 mixed_pings False model wh 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/AT36/gbin ref_method refsm refuv_inputfile a_at.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 wh300 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_at.gps ub_type 1920 uhdas_config yearbase = 2016 uhdas_dir = /home/data/AT36 sonar = wh300 gbin = /home/data/AT36/gbin gbinsonar = /home/data/AT36/gbin/wh300 raw = /home/data/AT36/raw rawsonar = /home/data/AT36/raw/wh300 rbin = /home/data/AT36/rbin proc = /home/data/AT36/proc procsonar = /home/data/AT36/proc/wh300 other attributes: gbin_params = hdg_inst : gyro hdg_inst_msgs : [('gyro', 'hdg'), ('phins', 'hdg'), ('phins2', 'hdg')] hdg_msg : hdg pitch_inst : pitch_msg : pos_inst : gpsnav pos_msg : gps roll_inst : roll_msg : hcorr = ['phins', 'hdg', 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 2016-08-07 10:59:31,253 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:31,253 INFO quick_adcp step 1: set up files in "edit" directory 2016-08-07 10:59:31,253 INFO quick_run file exists (edit/clearflags.tmp). not writing 2016-08-07 10:59:31,253 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:31,253 INFO quick_adcp step 2: scan files for time range 2016-08-07 10:59:31,253 DEBUG quick_npy Starting: scanping 2016-08-07 10:59:31,304 DEBUG quick_npy Ending: scanping 2016-08-07 10:59:31,304 DEBUG quick_subs start_end_time 2016/07/28 16:00:01 to 2016/07/28 15:59:59 2016-08-07 10:59:31,304 DEBUG quick_subs dd0: 209.666678 dd1: 209.666655 2016-08-07 10:59:31,304 INFO quick_adcp looking for database with adcpdb/a_at*.blk 2016-08-07 10:59:31,304 INFO quick_adcp database found: listing blocks 2016-08-07 10:59:31,305 DEBUG quick_subs removing a_atdir.blk 2016-08-07 10:59:31,305 DEBUG quick_subs about to run mkblkdir 2016-08-07 10:59:31,305 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-08-07 10:59:31,305 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-08-07 10:59:31,310 DEBUG quick_subs database passes. 2016-08-07 10:59:31,310 DEBUG quick_subs start_end_time 2016/07/28 15:59:43 to 2016/08/07 10:43:22 2016-08-07 10:59:31,310 DEBUG quick_subs dd0: 209.666470 dd1: 219.446782 2016-08-07 10:59:31,311 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2016-08-07 10:59:31,311 DEBUG quick_adcp origdb_time_range is 2016/07/28 15:59:43 to 2016/08/07 10:43:22 2016-08-07 10:59:31,311 DEBUG quick_adcp (209.666470 to 219.446782) 2016-08-07 10:59:31,311 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:31,311 INFO quick_adcp step 3: generate averaged data... 2016-08-07 10:59:31,311 INFO quick_run file load/ping_editparams.txt exists. not replacing 2016-08-07 10:59:31,311 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:31,311 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/load 2016-08-07 10:59:31,311 DEBUG quick_setup running python command "run_pingavg_npy" 2016-08-07 10:59:31,311 DEBUG quick_npy Starting: pingavg 2016-08-07 10:59:31,312 DEBUG quick_npy xducerxy is [0, 0] 2016-08-07 10:59:31,312 DEBUG quick_npy singleping editing parameters: 2016-08-07 10:59:31,312 DEBUG quick_npy bigtarget_mab_window : 11 2016-08-07 10:59:31,312 DEBUG quick_npy rl_endbin : 20 2016-08-07 10:59:31,312 DEBUG quick_npy max_search_depth : 500 2016-08-07 10:59:31,312 DEBUG quick_npy cor_cutoff : 70 2016-08-07 10:59:31,312 DEBUG quick_npy ampfilt : 40 2016-08-07 10:59:31,312 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2016-08-07 10:59:31,312 DEBUG quick_npy rl_startbin : 2 2016-08-07 10:59:31,312 DEBUG quick_npy ecutoff : 0.500000 2016-08-07 10:59:31,312 DEBUG quick_npy refavg_valcutoff : 1 2016-08-07 10:59:31,312 DEBUG quick_npy weakprof_percent : 50 2016-08-07 10:59:31,312 DEBUG quick_npy bigtarget_ampthresh : 55 2016-08-07 10:59:31,316 INFO pingavg ---------------- 2016-08-07 10:59:31,316 INFO pingavg sonar is wh300 2016-08-07 10:59:31,316 INFO pingavg Pingavg.run for time range 219.416667 to 219.456622 2016-08-07 10:59:31,316 INFO pingavg transducer offset: xducer_dx = 0.000, xducer_dy = 0.000 2016-08-07 10:59:31,316 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2016-08-07 10:59:31,316 INFO pingavg ---------------- 2016-08-07 10:59:31,328 DEBUG pingavg Chunk 1 of 1, 219.416667 to 219.456622 2016-08-07 10:59:31,328 DEBUG pingavg Nothing written 2016-08-07 10:59:31,329 DEBUG quick_npy wrote 0 averages 2016-08-07 10:59:31,329 DEBUG quick_npy Ending: pingavg 2016-08-07 10:59:31,329 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:31,329 INFO quick_adcp step 4: load averaged data (to database) 2016-08-07 10:59:31,329 DEBUG quick_subs in del_overlapping 2016-08-07 10:59:31,330 DEBUG quick_subs lastblock: 2016-08-07 10:59:31,330 DEBUG quick_subs 23 2016-08-07 10:59:31,330 DEBUG quick_subs lastcmd: 2016-08-07 10:59:31,330 DEBUG quick_subs 23 2016-08-07 10:59:31,330 DEBUG quick_subs delblks: 2016-08-07 10:59:31,330 DEBUG quick_subs [23] 2016-08-07 10:59:31,330 DEBUG quick_subs loadblks: 2016-08-07 10:59:31,330 DEBUG quick_subs [23] 2016-08-07 10:59:31,330 DEBUG quick_subs about to run mkblkdir 2016-08-07 10:59:31,330 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-08-07 10:59:31,330 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-08-07 10:59:31,335 DEBUG quick_subs database passes. 2016-08-07 10:59:31,335 DEBUG quick_subs start_end_time 2016/07/28 15:59:43 to 2016/08/07 10:11:22 2016-08-07 10:59:31,335 DEBUG quick_subs dd0: 209.666470 dd1: 219.424560 2016-08-07 10:59:31,335 DEBUG quick_run [23] 2016-08-07 10:59:31,335 DEBUG quick_run cmdlist 2016-08-07 10:59:31,335 DEBUG quick_run ['./ens_blk023.cmd'] 2016-08-07 10:59:31,335 INFO quick_run loaded time range: 2016/08/07 10:13:22 to 2016/08/07 10:57:23 2016-08-07 10:59:31,335 DEBUG quick_setup load/ldcodas.tmp exists 2016-08-07 10:59:31,336 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:31,336 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/load 2016-08-07 10:59:31,336 DEBUG quick_setup running python command "ldcodas" 2016-08-07 10:59:31,336 DEBUG quick_subs filling "thisload" timerange 2016-08-07 10:59:31,336 DEBUG quick_subs in ldcodas 2016-08-07 10:59:31,336 DEBUG quick_subs cmdlist: 2016-08-07 10:59:31,336 DEBUG quick_subs ['./ens_blk023.cmd'] 2016-08-07 10:59:31,336 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_at DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2016 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk023.cmd 2016-08-07 10:59:31,336 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2016-08-07 10:59:31,340 INFO quick_run 24 block files present 2016-08-07 10:59:31,340 DEBUG quick_subs removing a_atdir.blk 2016-08-07 10:59:31,340 DEBUG quick_subs about to run mkblkdir 2016-08-07 10:59:31,340 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-08-07 10:59:31,340 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-08-07 10:59:31,348 DEBUG quick_subs database passes. 2016-08-07 10:59:31,348 DEBUG quick_subs start_end_time 2016/07/28 15:59:43 to 2016/08/07 10:57:23 2016-08-07 10:59:31,348 DEBUG quick_subs dd0: 209.666470 dd1: 219.456516 2016-08-07 10:59:31,349 INFO quick_adcp database time range: 2016-08-07 10:59:31,349 INFO quick_adcp 2016/07/28 15:59:43 to 2016/08/07 10:57:23 2016-08-07 10:59:31,349 INFO quick_adcp (209.666470 to 219.456516) 2016-08-07 10:59:31,349 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:31,349 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/adcpdb 2016-08-07 10:59:31,349 DEBUG quick_setup running python command "lst_conf" 2016-08-07 10:59:31,349 DEBUG quick_subs dbname: a_at output: a_at.cnh time_ranges: all 2016-08-07 10:59:31,349 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2016-08-07 10:59:31,367 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:31,367 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2016-08-07 10:59:31,367 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2016-08-07 10:59:31,367 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:31,367 INFO quick_adcp step 6: run setflags? 2016-08-07 10:59:31,367 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:31,367 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/edit 2016-08-07 10:59:31,368 DEBUG quick_setup running python command "write_setflags" 2016-08-07 10:59:31,368 DEBUG quick_subs dbname: ../adcpdb/a_at pg_min: 50 set_range_bit time_ranges: all 2016-08-07 10:59:31,368 DEBUG quick_setup about to run setflags setflags.tmp 2016-08-07 10:59:31,390 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:31,391 INFO quick_adcp step 7: get navigation 2016-08-07 10:59:31,391 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:31,391 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/nav 2016-08-07 10:59:31,391 DEBUG quick_setup running python command "catnav" 2016-08-07 10:59:31,392 INFO quick_subs navigation file nav/a_at.gps created from load/*.gps2 2016-08-07 10:59:31,393 INFO quick_subs navigation file nav/a_at.agt created from load/*.gpst2 2016-08-07 10:59:31,395 DEBUG quick_mpl Starting plot: uvship 2016-08-07 10:59:31,633 DEBUG quick_mpl Ending plot: uvship 2016-08-07 10:59:31,633 INFO quick_run plotted uvship 2016-08-07 10:59:31,633 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:31,634 INFO quick_adcp step 8: list heading 2016-08-07 10:59:31,634 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2016-08-07 10:59:31,634 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:31,634 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/cal/rotate 2016-08-07 10:59:31,634 DEBUG quick_setup running python command "lst_hdg" 2016-08-07 10:59:31,634 DEBUG quick_subs dbname: ../../adcpdb/a_at output: scn.hdg step_size= 1 year_base= 2016 time_ranges: all 2016-08-07 10:59:31,634 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2016-08-07 10:59:31,650 INFO quick_run ... headings extracted 2016-08-07 10:59:31,651 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:31,651 INFO quick_adcp step 9: plot heading correction 2016-08-07 10:59:31,651 DEBUG quick_run hcorr_inst is phins 2016-08-07 10:59:31,651 DEBUG quick_mpl Starting plot: hcorr 2016-08-07 10:59:31,675 DEBUG quick_mpl found 9.790041 days of data 2016-08-07 10:59:31,675 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2016-08-07 10:59:31,675 DEBUG quick_mpl printing 3 pages 2016-08-07 10:59:32,050 DEBUG quick_mpl Ending plot: hcorr 2016-08-07 10:59:32,050 INFO quick_run plots are in cal/rotate/*png 2016-08-07 10:59:32,050 INFO quick_adcp ------------------------- 2016-08-07 10:59:32,050 INFO quick_adcp ---- running navsteps --- 2016-08-07 10:59:32,050 INFO quick_adcp ------------------------- 2016-08-07 10:59:32,050 INFO quick_adcp step 10: nav steps: run adcpsect 2016-08-07 10:59:32,050 INFO quick_adcp navstep 1 2016-08-07 10:59:32,050 DEBUG quick_setup nav/as_nav.tmp exists 2016-08-07 10:59:32,050 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:32,050 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/nav 2016-08-07 10:59:32,050 DEBUG quick_setup running python command "as_nav" 2016-08-07 10:59:32,050 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at 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 2016/07/28 15:59:43 to 2016/08/07 10:57:23 /* the whole time range */ 2016-08-07 10:59:32,050 DEBUG quick_setup about to run adcpsect as_nav.tmp 2016-08-07 10:59:32,078 INFO quick_run ... ran adcpsect for navsteps 2016-08-07 10:59:32,078 INFO quick_adcp ------------------------- 2016-08-07 10:59:32,078 INFO quick_adcp step 11: nav steps: run refabs 2016-08-07 10:59:32,078 INFO quick_adcp navstep 2 2016-08-07 10:59:32,078 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:32,078 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/nav 2016-08-07 10:59:32,078 DEBUG quick_setup running python command "refabs" 2016-08-07 10:59:32,078 DEBUG quick_subs fix_file_type: simple reference_file: a_at.nav fix_file: a_at.gps output: a_at.ref year_base= 2016 ensemble_length= 120 gap_tolerance= 10 2016-08-07 10:59:32,078 DEBUG quick_setup about to run refabs refabs.tmp 2016-08-07 10:59:32,107 INFO quick_run ... ran refabs for navsteps 2016-08-07 10:59:32,107 INFO quick_adcp ------------------------- 2016-08-07 10:59:32,107 INFO quick_adcp step 12: nav steps: run smoothr for plots 2016-08-07 10:59:32,107 INFO quick_adcp navstep 3 2016-08-07 10:59:32,107 DEBUG quick_setup nav/smoothr.tmp exists 2016-08-07 10:59:32,107 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:32,107 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/nav 2016-08-07 10:59:32,107 DEBUG quick_setup running python command "smoothr" 2016-08-07 10:59:32,108 DEBUG quick_subs reference_file: a_at.nav refabs_output: a_at.ref output: a_at.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= 120 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2016-08-07 10:59:32,108 DEBUG quick_setup about to run smoothr smoothr.tmp 2016-08-07 10:59:32,239 INFO quick_run ... ran smoothr 2016-08-07 10:59:32,239 INFO quick_adcp ------------------------- 2016-08-07 10:59:32,239 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2016-08-07 10:59:32,239 INFO quick_adcp navstep 4 2016-08-07 10:59:32,239 INFO quick_run smoothing method for ship speed: refsm 2016-08-07 10:59:32,239 INFO quick_run smoothing window: 3 2016-08-07 10:59:32,239 INFO quick_run ship speed source: nav 2016-08-07 10:59:32,239 DEBUG quick_npy Starting: refsm 2016-08-07 10:59:32,371 DEBUG quick_npy Ending: refsm 2016-08-07 10:59:32,371 INFO quick_run ... shipspeed smoothing step done 2016-08-07 10:59:32,371 INFO quick_adcp ------------------------- 2016-08-07 10:59:32,371 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2016-08-07 10:59:32,371 INFO quick_adcp navstep 5 2016-08-07 10:59:32,371 DEBUG quick_setup nav/put_txy.tmp exists 2016-08-07 10:59:32,371 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:32,371 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/nav 2016-08-07 10:59:32,371 DEBUG quick_setup running python command "put_txy" 2016-08-07 10:59:32,372 DEBUG quick_subs dbname: ../adcpdb/a_at position_file: a_at.gps year_base= 2016 tolerance= 5 2016-08-07 10:59:32,372 DEBUG quick_setup about to run put_txy put_txy.tmp 2016-08-07 10:59:32,392 INFO quick_run ... ran put_txy 2016-08-07 10:59:32,392 DEBUG quick_setup nav/put_tuv.tmp exists 2016-08-07 10:59:32,392 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:32,392 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/nav 2016-08-07 10:59:32,392 DEBUG quick_setup running python command "put_tuv" 2016-08-07 10:59:32,393 DEBUG quick_subs dbname: ../adcpdb/a_at shipspeed_file: refsm_tuv.asc year_base= 2016 tolerance= 5 2016-08-07 10:59:32,393 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2016-08-07 10:59:32,415 INFO quick_run ... ran put_tuv 2016-08-07 10:59:32,415 DEBUG quick_mpl Starting plot: nav 2016-08-07 10:59:32,584 DEBUG quick_mpl Ending plot: nav 2016-08-07 10:59:32,584 INFO quick_run ... made navigation plot 2016-08-07 10:59:32,584 INFO quick_adcp ------------------------- 2016-08-07 10:59:32,584 INFO quick_adcp step 15: nav steps: make reflayer plots 2016-08-07 10:59:32,584 INFO quick_adcp navstep 6 2016-08-07 10:59:32,584 DEBUG quick_mpl Starting plot: refl 2016-08-07 10:59:32,652 DEBUG quick_mpl found 9.785841 days of data 2016-08-07 10:59:32,652 DEBUG quick_mpl start day is 209.000000 2016-08-07 10:59:32,652 DEBUG quick_mpl figures with 2.000000 days per page 2016-08-07 10:59:32,652 DEBUG quick_mpl printing 6 pages 2016-08-07 10:59:32,652 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2016-08-07 10:59:33,005 DEBUG quick_mpl Ending plot: refl 2016-08-07 10:59:33,005 INFO quick_run ... made reflayer plots 2016-08-07 10:59:33,005 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:33,005 INFO quick_adcp step 10: find profile flags 2016-08-07 10:59:33,005 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:33,005 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/edit 2016-08-07 10:59:33,005 DEBUG quick_setup running python command "run_autoedit_npy" 2016-08-07 10:59:33,005 DEBUG quick_npy Starting: autoedit 2016-08-07 10:59:33,098 DEBUG pingedit wrote 63 bad bins to abadbin_tmp.asc 2016-08-07 10:59:33,107 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2016-08-07 10:59:33,107 DEBUG quick_npy Ending: autoedit 2016-08-07 10:59:33,107 INFO quick_run ... extracted files using automatic editing 2016-08-07 10:59:33,107 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:33,107 INFO quick_adcp step 11: apply editing 2016-08-07 10:59:33,107 DEBUG quick_run starting in: /home/data/AT36/proc/wh300 2016-08-07 10:59:33,107 DEBUG quick_run executing commands from: edit 2016-08-07 10:59:33,108 DEBUG quick_run about to run dbupdate ../adcpdb/a_at abadprf_tmp.asc 2016-08-07 10:59:33,111 DEBUG quick_run about to run badbin ../adcpdb/a_at abadbin_tmp.asc 2016-08-07 10:59:33,115 DEBUG quick_subs dbname: ../adcpdb/a_at pg_min: 50 set_range_bit time_ranges: all 2016-08-07 10:59:33,115 DEBUG quick_run about to run setflags setflags.tmp 2016-08-07 10:59:33,141 DEBUG quick_run changing directories back to /home/data/AT36/proc/wh300 2016-08-07 10:59:33,141 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:33,141 INFO quick_adcp step 12: run calibration steps 2016-08-07 10:59:33,142 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2016-08-07 10:59:33,142 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:33,142 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/cal/botmtrk 2016-08-07 10:59:33,142 DEBUG quick_setup running python command "lst_btrk" 2016-08-07 10:59:33,142 DEBUG quick_subs dbname: ../../adcpdb/a_at output: a_at.btm step_size= 1 year_base= 2016 time_ranges: 2016/07/28 15:59:43 to 2016/08/07 10:57:23 /* whole time range */ 2016-08-07 10:59:33,142 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2016-08-07 10:59:33,151 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2016-08-07 10:59:33,152 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:33,152 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/cal/botmtrk 2016-08-07 10:59:33,152 DEBUG quick_setup running python command "refabsbt" 2016-08-07 10:59:33,152 DEBUG quick_subs fix_file_type: simple reference_file: a_at.btm fix_file: ../../nav/a_at.gps output: a_at.ref year_base= 2016 ensemble_length= 120 gap_tolerance= 60 2016-08-07 10:59:33,152 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2016-08-07 10:59:33,168 INFO quick_run ...bottom track info in check cal/botmtrk 2016-08-07 10:59:33,168 DEBUG quick_mpl Starting plot: btcal 2016-08-07 10:59:33,401 DEBUG quick_mpl Ending plot: btcal 2016-08-07 10:59:33,401 DEBUG quick_setup nav/as_nav.tmp exists 2016-08-07 10:59:33,401 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:33,401 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/nav 2016-08-07 10:59:33,401 DEBUG quick_setup running python command "as_nav" 2016-08-07 10:59:33,401 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at 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 2016/07/28 15:59:43 to 2016/08/07 10:57:23 /* the whole time range */ 2016-08-07 10:59:33,401 DEBUG quick_setup about to run adcpsect as_nav.tmp 2016-08-07 10:59:33,433 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2016-08-07 10:59:33,433 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:33,433 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/cal/watertrk 2016-08-07 10:59:33,433 DEBUG quick_setup running python command "timslip" 2016-08-07 10:59:33,433 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_at.gps reference_file: ../../nav/a_at.nav output_file: a_at_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 2016-08-07 10:59:33,433 DEBUG quick_setup about to run timslip timslip.tmp 2016-08-07 10:59:33,446 INFO quick_run ... watertrack info in cal/watertrk 2016-08-07 10:59:33,447 DEBUG quick_mpl Starting plot: wtcal 2016-08-07 10:59:33,448 DEBUG quick_mpl Found 28 calibration points 2016-08-07 10:59:33,875 DEBUG quick_mpl Ending plot: wtcal 2016-08-07 10:59:33,875 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:33,875 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/cal/watertrk 2016-08-07 10:59:33,875 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2016-08-07 10:59:33,875 DEBUG quick_npy Starting: guess_xducerxy 2016-08-07 10:59:33,955 DEBUG quick_npy Ending: guess_xducerxy 2016-08-07 10:59:33,955 INFO quick_run ... check cal/watertrk for estimate 2016-08-07 10:59:33,955 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:33,955 INFO quick_adcp step 13: extract and plot temperature 2016-08-07 10:59:33,955 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:33,955 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/edit 2016-08-07 10:59:33,955 DEBUG quick_setup running python command "lst_temp" 2016-08-07 10:59:33,955 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at.tem step_size= 1 year_base= 2016 time_ranges: all 2016-08-07 10:59:33,956 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2016-08-07 10:59:33,977 DEBUG quick_mpl Starting plot: temp 2016-08-07 10:59:34,001 DEBUG quick_mpl plotting 6318 points 2016-08-07 10:59:34,125 DEBUG quick_mpl Ending plot: temp 2016-08-07 10:59:34,125 INFO quick_run plotted temperature 2016-08-07 10:59:34,125 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:34,125 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2016-08-07 10:59:34,125 DEBUG quick_setup edit/lst_npings.tmp exists 2016-08-07 10:59:34,125 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:34,125 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/edit 2016-08-07 10:59:34,125 DEBUG quick_setup running python command "lst_npings" 2016-08-07 10:59:34,125 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at_npings.txt step_size= 1 year_base= 2016 time_ranges: all 2016-08-07 10:59:34,125 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2016-08-07 10:59:34,142 DEBUG quick_mpl Starting plot: npings 2016-08-07 10:59:34,162 DEBUG quick_mpl plotting 6318 points 2016-08-07 10:59:34,238 DEBUG quick_mpl Ending plot: npings 2016-08-07 10:59:34,238 INFO quick_run ... plotted number of pings per ensemble 2016-08-07 10:59:34,238 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:34,238 INFO quick_adcp step 15: extract matlab "allbins" 2016-08-07 10:59:34,238 DEBUG quick_asect step 18: make matlab files for plotting 2016-08-07 10:59:34,238 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:34,238 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/vector 2016-08-07 10:59:34,238 DEBUG quick_setup running python command "timegrid" 2016-08-07 10:59:34,239 DEBUG quick_setup about to run timegrid a_at.tmp 2016-08-07 10:59:34,242 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:34,242 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/vector 2016-08-07 10:59:34,242 DEBUG quick_setup running python command "as_vect" 2016-08-07 10:59:34,243 DEBUG quick_setup about to run adcpsect as_vect.tmp 2016-08-07 10:59:34,276 DEBUG quick_asect done making vector matfiles 2016-08-07 10:59:34,277 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:34,277 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/contour 2016-08-07 10:59:34,277 DEBUG quick_setup running python command "timegrid" 2016-08-07 10:59:34,277 DEBUG quick_setup about to run timegrid a_at.tmp 2016-08-07 10:59:34,281 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:34,281 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/contour 2016-08-07 10:59:34,281 DEBUG quick_setup running python command "as_cont" 2016-08-07 10:59:34,281 DEBUG quick_setup about to run adcpsect as_cont.tmp 2016-08-07 10:59:34,335 DEBUG quick_setup starting in /home/data/AT36/proc/wh300 2016-08-07 10:59:34,336 DEBUG quick_setup executing commands from /home/data/AT36/proc/wh300/contour 2016-08-07 10:59:34,336 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_at 2016-08-07 10:59:34,495 DEBUG quick_asect done running getmat with "allbins" 2016-08-07 10:59:34,495 INFO quick_adcp --------------------------------------------- 2016-08-07 10:59:34,495 INFO quick_adcp writing "cruise_info.txt" 2016-08-07 10:59:34,501 INFO root copying NOFIG to /home/adcp/www/figures/wh300_hcorr_plot.png 2016-08-07 10:59:34,501 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/wh300_hcorr_plot_thumb.png 2016-08-07 10:59:34,502 DEBUG root matfile is contour/contour_uv.mat 2016-08-07 10:59:34,503 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/wh300_cont_uv.mat 2016-08-07 10:59:34,503 DEBUG root matfile is vector/vector_uv.mat 2016-08-07 10:59:34,503 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/wh300_vect_uv.mat 2016-08-07 10:59:34,503 DEBUG root matfile is contour/contour_xy.mat 2016-08-07 10:59:34,503 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/wh300_cont_xy.mat 2016-08-07 10:59:34,504 DEBUG root matfile is vector/vector_xy.mat 2016-08-07 10:59:34,504 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/wh300_vect_xy.mat 2016-08-07 10:59:34,504 DEBUG root about to copy file edit/a_at.tem to /home/adcp/www/data/wh300_temp.asc 2016-08-07 10:59:34,504 INFO root copying edit/a_at.tem to /home/adcp/www/data/wh300_temp.asc 2016-08-07 10:59:34,509 INFO netcdf Using pupynere. 2016-08-07 10:59:34,601 DEBUG root about to copy netcdf file /home/data/AT36/proc/wh300/contour/wh300.nc to /home/adcp/www/data/wh300.nc 2016-08-07 10:59:34,606 INFO root copying edit/a_at.tem to /home/adcp/www/data/wh300.nc 2016-08-07 10:59:34,627 INFO root generating pingstats for wh300 2016-08-07 10:59:34,627 INFO root Ending quick_adcp.py