2015-11-14 20:03:49,057 DEBUG root about to write control file parameters to --yearbase 2015 --cruisename HI1602 --configtype python --sonar os75bb --dbname a_hi --datatype uhdas --cfgpath /home/data/HI1602/proc/os75bb/config --ens_len 300 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea # xducer_dx, xducer_dy not set ## see config/HI1602_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 2015-11-14 20:03:49,057 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d os75bb 2015-11-14 20:03:49,061 DEBUG quick_setup found cruise_info.hcorr (posmv, pmv, 0) 2015-11-14 20:03:49,061 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2015-11-14 20:03:49,062 INFO quick_setup fix file is a_hi.gps 2015-11-14 20:03:49,062 INFO quick_setup reflayer: ref_method = refsm 2015-11-14 20:03:49,063 INFO quick_setup reflayer: refuv_source = nav 2015-11-14 20:03:49,063 INFO quick_setup reflayer: refuv_smoothwin = 3 2015-11-14 20:03:49,063 INFO quick_adcp importing numpy version 1.8.2 2015-11-14 20:03:49,089 INFO quick_adcp importing matplotlib version 1.3.1 2015-11-14 20:03:49,439 DEBUG quick_mpl in Q_mpl 2015-11-14 20:03:49,439 INFO quick_adcp ===================================================== 2015-11-14 20:03:49,440 INFO quick_adcp ===================================================== 2015-11-14 20:03:49,440 INFO quick_adcp command line was: /home/currents/programs/uhdas/scripts/run_quick.py -d os75bb 2015-11-14 20:03:49,440 INFO quick_adcp cwd is /home/data/HI1602/proc/os75bb 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 2015-11-14 20:03:49,440 DEBUG quick_asect extracting matlab files for os75, bb pings 2015-11-14 20:03:49,468 DEBUG quick_setup data directory: /home/data/HI1602/raw/os75 2015-11-14 20:03:49,470 INFO quick_setup found 158 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/HI1602/raw/os75/*.raw" 2015-11-14 20:03:49,471 DEBUG quick_setup found 158 files from original filelist 2015-11-14 20:03:49,471 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/HI1602/raw/os75/hi2015_304_69526.raw ... 2015-11-14 20:03:49,473 DEBUG quick_adcp Sat Nov 14 20:03:49 2015 running quick_adcp.py as follows: --cntfile /home/data/HI1602/proc/os75bb/os75bb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_hi 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 21 gridnum 80 increment 10 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2015 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/HI1602/proc/os75bb/config cntfile /home/data/HI1602/proc/os75bb/os75bb_qpy.cnt commands None configtype python cruisename HI1602 data_def vmadcp.def datadir /home/data/HI1602/raw/os75 datafile_glob *.raw datatype uhdas dbname a_hi dday_bailout None debug False ens_len 300 expert None filelist ['/home/data/HI1602/raw/os75/hi2015_304_69526.raw', '/home/data/HI1602/raw/os75/hi2015_304_72000.raw', '/home/data/HI1602/raw/os75/hi2015_304_79200.raw', '/home/data/HI1602/raw/os75/hi2015_305_00000.raw', '/home/data/HI1602/raw/os75/hi2015_305_07200.raw', '/home/data/HI1602/raw/os75/hi2015_305_14400.raw', 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find_pflags True firstdepth 21 fixfile a_hi.gps fixfilexy a_hi.agt frequency 75 hcorr_inst posmv help False incremental True instname os75 jitter 15 max_BLKprofiles 300 max_search_depth 2000 maxrunsecs None min_filter_fraction 0.5 model os nosave_editcfg 0 numbins 128 pgmin 50 ping_headcorr True pingtype bb printformats png proc_engine python proc_yearbase 2015 py_gbindirbase /home/data/HI1602/gbin ref_method refsm refuv_inputfile a_hi.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 os75bb 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_hi.gps ub_type 1920 uhdas_config yearbase = 2015 uhdas_dir = /home/data/HI1602 sonar = os75bb gbin = /home/data/HI1602/gbin gbinsonar = /home/data/HI1602/gbin/os75 raw = /home/data/HI1602/raw rawsonar = /home/data/HI1602/raw/os75 rbin = /home/data/HI1602/rbin proc = /home/data/HI1602/proc procsonar = /home/data/HI1602/proc/os75bb other attributes: gbin_params = hdg_inst : gyro hdg_inst_msgs : [('gyro', 'hnc'), ('posmv', 'pmv'), ('gyro_merid', 'hdg')] hdg_msg : hnc pitch_inst : posmv pitch_msg : pmv pos_inst : gpsnav pos_msg : gps roll_inst : posmv roll_msg : pmv pingavg_params = hbest : ['gyro', 'hnc'] head_align : 46.05 tr_depth : 5 velscale : {'scale': 1.0} 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 2015 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 2015-11-14 20:03:49,473 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:49,474 INFO quick_adcp step 1: set up files in "edit" directory 2015-11-14 20:03:49,474 INFO quick_run file exists (edit/clearflags.tmp). not writing 2015-11-14 20:03:49,474 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:49,474 INFO quick_adcp step 2: scan files for time range 2015-11-14 20:03:49,474 DEBUG quick_npy Starting: scanping 2015-11-14 20:03:49,741 DEBUG quick_npy Ending: scanping 2015-11-14 20:03:49,742 DEBUG quick_subs start_end_time 2015/11/01 19:18:51 to 2015/11/01 19:29:01 2015-11-14 20:03:49,742 DEBUG quick_subs dd0: 304.804757 dd1: 304.811817 2015-11-14 20:03:49,742 INFO quick_adcp looking for database with adcpdb/a_hi*.blk 2015-11-14 20:03:49,743 INFO quick_adcp database found: listing blocks 2015-11-14 20:03:49,743 DEBUG quick_subs removing a_hidir.blk 2015-11-14 20:03:49,743 DEBUG quick_subs about to run mkblkdir 2015-11-14 20:03:49,743 DEBUG quick_subs database still exists; rerunning mkdirblk 2015-11-14 20:03:49,743 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2015-11-14 20:03:49,751 DEBUG quick_subs database passes. 2015-11-14 20:03:49,752 DEBUG quick_subs start_end_time 2015/11/01 19:23:48 to 2015/11/14 19:43:48 2015-11-14 20:03:49,752 DEBUG quick_subs dd0: 304.808194 dd1: 317.822083 2015-11-14 20:03:49,752 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2015-11-14 20:03:49,752 DEBUG quick_adcp origdb_time_range is 2015/11/01 19:23:48 to 2015/11/14 19:43:48 2015-11-14 20:03:49,752 DEBUG quick_adcp (304.808194 to 317.822083) 2015-11-14 20:03:49,752 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:49,752 INFO quick_adcp step 3: generate averaged data... 2015-11-14 20:03:49,752 INFO quick_run file load/ping_editparams.txt exists. not replacing 2015-11-14 20:03:49,752 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:49,753 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/load 2015-11-14 20:03:49,753 DEBUG quick_setup running python command "run_pingavg_npy" 2015-11-14 20:03:49,753 DEBUG quick_npy Starting: pingavg 2015-11-14 20:03:49,754 DEBUG quick_npy singleping editing parameters: 2015-11-14 20:03:49,755 DEBUG quick_npy bigtarget_mab_window : 11 2015-11-14 20:03:49,755 DEBUG quick_npy rl_endbin : 20 2015-11-14 20:03:49,755 DEBUG quick_npy max_search_depth : 2000 2015-11-14 20:03:49,755 DEBUG quick_npy cor_cutoff : 120 2015-11-14 20:03:49,755 DEBUG quick_npy ampfilt : 40 2015-11-14 20:03:49,755 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2015-11-14 20:03:49,755 DEBUG quick_npy rl_startbin : 2 2015-11-14 20:03:49,755 DEBUG quick_npy ecutoff : 0.800000 2015-11-14 20:03:49,755 DEBUG quick_npy refavg_valcutoff : 1 2015-11-14 20:03:49,755 DEBUG quick_npy weakprof_percent : 30 2015-11-14 20:03:49,755 DEBUG quick_npy bigtarget_ampthresh : 55 2015-11-14 20:03:49,755 DEBUG quick_npy xducerxy is [0, 0] 2015-11-14 20:03:49,761 INFO pingavg ---------------- 2015-11-14 20:03:49,761 INFO pingavg Pingavg.run for time range 317.750016 to 317.832694 2015-11-14 20:03:49,761 INFO pingavg transducer offset: xducer_dx = 0.000, xducer_dy = 0.000 2015-11-14 20:03:49,761 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2015-11-14 20:03:49,761 INFO pingavg ---------------- 2015-11-14 20:03:49,787 DEBUG pingavg Chunk 1 of 1, 317.750016 to 317.832694 2015-11-14 20:03:49,787 DEBUG pingavg Nothing written 2015-11-14 20:03:49,787 DEBUG quick_npy wrote 0 averages 2015-11-14 20:03:49,788 DEBUG quick_npy Ending: pingavg 2015-11-14 20:03:49,788 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:49,788 INFO quick_adcp step 4: load averaged data (to database) 2015-11-14 20:03:49,789 DEBUG quick_subs in del_overlapping 2015-11-14 20:03:49,789 DEBUG quick_subs lastblock: 2015-11-14 20:03:49,789 DEBUG quick_subs 13 2015-11-14 20:03:49,789 DEBUG quick_subs lastcmd: 2015-11-14 20:03:49,789 DEBUG quick_subs 13 2015-11-14 20:03:49,789 DEBUG quick_subs delblks: 2015-11-14 20:03:49,789 DEBUG quick_subs [13] 2015-11-14 20:03:49,789 DEBUG quick_subs loadblks: 2015-11-14 20:03:49,789 DEBUG quick_subs [13] 2015-11-14 20:03:49,790 DEBUG quick_subs about to run mkblkdir 2015-11-14 20:03:49,790 DEBUG quick_subs database still exists; rerunning mkdirblk 2015-11-14 20:03:49,790 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2015-11-14 20:03:49,798 DEBUG quick_subs database passes. 2015-11-14 20:03:49,798 DEBUG quick_subs start_end_time 2015/11/01 19:23:48 to 2015/11/14 07:18:47 2015-11-14 20:03:49,798 DEBUG quick_subs dd0: 304.808194 dd1: 317.304711 2015-11-14 20:03:49,798 DEBUG quick_run [13] 2015-11-14 20:03:49,798 DEBUG quick_run cmdlist 2015-11-14 20:03:49,798 DEBUG quick_run ['./ens_blk013.cmd'] 2015-11-14 20:03:49,800 INFO quick_run loaded time range: 2015/11/14 07:23:49 to 2015/11/14 19:58:49 2015-11-14 20:03:49,800 DEBUG quick_setup load/ldcodas.tmp exists 2015-11-14 20:03:49,800 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:49,800 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/load 2015-11-14 20:03:49,800 DEBUG quick_setup running python command "ldcodas" 2015-11-14 20:03:49,800 DEBUG quick_subs filling "thisload" timerange 2015-11-14 20:03:49,801 DEBUG quick_subs in ldcodas 2015-11-14 20:03:49,801 DEBUG quick_subs cmdlist: 2015-11-14 20:03:49,801 DEBUG quick_subs ['./ens_blk013.cmd'] 2015-11-14 20:03:49,801 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_hi DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2015 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk013.cmd 2015-11-14 20:03:49,801 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2015-11-14 20:03:49,826 INFO quick_run 14 block files present 2015-11-14 20:03:49,826 DEBUG quick_subs removing a_hidir.blk 2015-11-14 20:03:49,826 DEBUG quick_subs about to run mkblkdir 2015-11-14 20:03:49,826 DEBUG quick_subs database still exists; rerunning mkdirblk 2015-11-14 20:03:49,826 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2015-11-14 20:03:49,834 DEBUG quick_subs database passes. 2015-11-14 20:03:49,834 DEBUG quick_subs start_end_time 2015/11/01 19:23:48 to 2015/11/14 19:58:49 2015-11-14 20:03:49,834 DEBUG quick_subs dd0: 304.808194 dd1: 317.832512 2015-11-14 20:03:49,834 INFO quick_adcp database time range: 2015-11-14 20:03:49,834 INFO quick_adcp 2015/11/01 19:23:48 to 2015/11/14 19:58:49 2015-11-14 20:03:49,834 INFO quick_adcp (304.808194 to 317.832512) 2015-11-14 20:03:49,835 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:49,835 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/adcpdb 2015-11-14 20:03:49,835 DEBUG quick_setup running python command "lst_conf" 2015-11-14 20:03:49,835 DEBUG quick_subs dbname: a_hi output: a_hi.cnh time_ranges: all 2015-11-14 20:03:49,835 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2015-11-14 20:03:49,854 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:49,854 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2015-11-14 20:03:49,854 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2015-11-14 20:03:49,854 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:49,854 INFO quick_adcp step 6: run setflags? 2015-11-14 20:03:49,854 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:49,855 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/edit 2015-11-14 20:03:49,855 DEBUG quick_setup running python command "write_setflags" 2015-11-14 20:03:49,855 DEBUG quick_subs dbname: ../adcpdb/a_hi pg_min: 50 set_range_bit time_ranges: all 2015-11-14 20:03:49,855 DEBUG quick_setup about to run setflags setflags.tmp 2015-11-14 20:03:49,900 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:49,900 INFO quick_adcp step 7: get navigation 2015-11-14 20:03:49,900 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:49,900 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/nav 2015-11-14 20:03:49,900 DEBUG quick_setup running python command "catnav" 2015-11-14 20:03:49,902 INFO quick_subs navigation file nav/a_hi.gps created from load/*.gps2 2015-11-14 20:03:49,903 INFO quick_subs navigation file nav/a_hi.agt created from load/*.gpst2 2015-11-14 20:03:49,905 DEBUG quick_mpl Starting plot: uvship 2015-11-14 20:03:50,616 DEBUG quick_mpl Ending plot: uvship 2015-11-14 20:03:50,616 INFO quick_run plotted uvship 2015-11-14 20:03:50,616 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:50,616 INFO quick_adcp step 8: list heading 2015-11-14 20:03:50,617 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2015-11-14 20:03:50,617 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:50,617 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/cal/rotate 2015-11-14 20:03:50,617 DEBUG quick_setup running python command "lst_hdg" 2015-11-14 20:03:50,617 DEBUG quick_subs dbname: ../../adcpdb/a_hi output: scn.hdg step_size= 1 year_base= 2015 time_ranges: all 2015-11-14 20:03:50,618 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2015-11-14 20:03:50,668 INFO quick_run ... headings extracted 2015-11-14 20:03:50,669 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:50,669 INFO quick_adcp step 9: plot heading correction 2015-11-14 20:03:50,669 DEBUG quick_run hcorr_inst is posmv 2015-11-14 20:03:50,669 DEBUG quick_mpl Starting plot: hcorr 2015-11-14 20:03:50,701 DEBUG quick_mpl found 13.024311 days of data 2015-11-14 20:03:50,702 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2015-11-14 20:03:50,702 DEBUG quick_mpl printing 4 pages 2015-11-14 20:03:51,424 DEBUG quick_mpl Ending plot: hcorr 2015-11-14 20:03:51,424 INFO quick_run plots are in cal/rotate/*png 2015-11-14 20:03:51,424 INFO quick_adcp ------------------------- 2015-11-14 20:03:51,424 INFO quick_adcp ---- running navsteps --- 2015-11-14 20:03:51,424 INFO quick_adcp ------------------------- 2015-11-14 20:03:51,424 INFO quick_adcp step 10: nav steps: run adcpsect 2015-11-14 20:03:51,424 INFO quick_adcp navstep 1 2015-11-14 20:03:51,424 DEBUG quick_setup nav/as_nav.tmp exists 2015-11-14 20:03:51,424 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:51,424 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/nav 2015-11-14 20:03:51,424 DEBUG quick_setup running python command "as_nav" 2015-11-14 20:03:51,425 DEBUG quick_subs dbname: ../adcpdb/a_hi output: a_hi step_size: 1 ndepth: 20 time_ranges: separate year_base= 2015 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 2015/11/01 19:23:48 to 2015/11/14 19:58:49 /* the whole time range */ 2015-11-14 20:03:51,425 DEBUG quick_setup about to run adcpsect as_nav.tmp 2015-11-14 20:03:51,482 INFO quick_run ... ran adcpsect for navsteps 2015-11-14 20:03:51,483 INFO quick_adcp ------------------------- 2015-11-14 20:03:51,483 INFO quick_adcp step 11: nav steps: run refabs 2015-11-14 20:03:51,483 INFO quick_adcp navstep 2 2015-11-14 20:03:51,483 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:51,483 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/nav 2015-11-14 20:03:51,483 DEBUG quick_setup running python command "refabs" 2015-11-14 20:03:51,483 DEBUG quick_subs fix_file_type: simple reference_file: a_hi.nav fix_file: a_hi.gps output: a_hi.ref year_base= 2015 ensemble_length= 300 gap_tolerance= 10 2015-11-14 20:03:51,484 DEBUG quick_setup about to run refabs refabs.tmp 2015-11-14 20:03:51,513 INFO quick_run ... ran refabs for navsteps 2015-11-14 20:03:51,513 INFO quick_adcp ------------------------- 2015-11-14 20:03:51,513 INFO quick_adcp step 12: nav steps: run smoothr for plots 2015-11-14 20:03:51,513 INFO quick_adcp navstep 3 2015-11-14 20:03:51,514 DEBUG quick_setup nav/smoothr.tmp exists 2015-11-14 20:03:51,514 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:51,514 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/nav 2015-11-14 20:03:51,514 DEBUG quick_setup running python command "smoothr" 2015-11-14 20:03:51,514 DEBUG quick_subs reference_file: a_hi.nav refabs_output: a_hi.ref output: a_hi.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 2015-11-14 20:03:51,514 DEBUG quick_setup about to run smoothr smoothr.tmp 2015-11-14 20:03:51,716 INFO quick_run ... ran smoothr 2015-11-14 20:03:51,717 INFO quick_adcp ------------------------- 2015-11-14 20:03:51,717 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2015-11-14 20:03:51,717 INFO quick_adcp navstep 4 2015-11-14 20:03:51,717 INFO quick_run smoothing method for ship speed: refsm 2015-11-14 20:03:51,717 INFO quick_run smoothing window: 3 2015-11-14 20:03:51,717 INFO quick_run ship speed source: nav 2015-11-14 20:03:51,718 DEBUG quick_npy Starting: refsm 2015-11-14 20:03:52,108 DEBUG quick_npy Ending: refsm 2015-11-14 20:03:52,108 INFO quick_run ... shipspeed smoothing step done 2015-11-14 20:03:52,109 INFO quick_adcp ------------------------- 2015-11-14 20:03:52,109 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2015-11-14 20:03:52,109 INFO quick_adcp navstep 5 2015-11-14 20:03:52,109 DEBUG quick_setup nav/put_txy.tmp exists 2015-11-14 20:03:52,109 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:52,109 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/nav 2015-11-14 20:03:52,110 DEBUG quick_setup running python command "put_txy" 2015-11-14 20:03:52,110 DEBUG quick_subs dbname: ../adcpdb/a_hi position_file: a_hi.gps year_base= 2015 tolerance= 5 2015-11-14 20:03:52,110 DEBUG quick_setup about to run put_txy put_txy.tmp 2015-11-14 20:03:52,179 INFO quick_run ... ran put_txy 2015-11-14 20:03:52,180 DEBUG quick_setup nav/put_tuv.tmp exists 2015-11-14 20:03:52,180 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:52,180 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/nav 2015-11-14 20:03:52,180 DEBUG quick_setup running python command "put_tuv" 2015-11-14 20:03:52,180 DEBUG quick_subs dbname: ../adcpdb/a_hi shipspeed_file: refsm_tuv.asc year_base= 2015 tolerance= 5 2015-11-14 20:03:52,181 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2015-11-14 20:03:52,239 INFO quick_run ... ran put_tuv 2015-11-14 20:03:52,240 DEBUG quick_mpl Starting plot: nav 2015-11-14 20:03:52,797 DEBUG quick_mpl Ending plot: nav 2015-11-14 20:03:52,797 INFO quick_run ... made navigation plot 2015-11-14 20:03:52,797 INFO quick_adcp ------------------------- 2015-11-14 20:03:52,798 INFO quick_adcp step 15: nav steps: make reflayer plots 2015-11-14 20:03:52,798 INFO quick_adcp navstep 6 2015-11-14 20:03:52,798 DEBUG quick_mpl Starting plot: refl 2015-11-14 20:03:52,936 DEBUG quick_mpl found 13.017333 days of data 2015-11-14 20:03:52,936 DEBUG quick_mpl start day is 304.000000 2015-11-14 20:03:52,936 DEBUG quick_mpl figures with 2.000000 days per page 2015-11-14 20:03:52,936 DEBUG quick_mpl printing 7 pages 2015-11-14 20:03:52,937 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2015-11-14 20:03:53,704 DEBUG quick_mpl Ending plot: refl 2015-11-14 20:03:53,704 INFO quick_run ... made reflayer plots 2015-11-14 20:03:53,705 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:53,705 INFO quick_adcp step 10: find profile flags 2015-11-14 20:03:53,705 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:53,705 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/edit 2015-11-14 20:03:53,705 DEBUG quick_setup running python command "run_autoedit_npy" 2015-11-14 20:03:53,705 DEBUG quick_npy Starting: autoedit 2015-11-14 20:03:53,855 DEBUG pingedit wrote 22 bad bins to abadbin_tmp.asc 2015-11-14 20:03:53,873 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2015-11-14 20:03:53,873 DEBUG quick_npy Ending: autoedit 2015-11-14 20:03:53,873 INFO quick_run ... extracted files using automatic editing 2015-11-14 20:03:53,873 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:53,874 INFO quick_adcp step 11: apply editing 2015-11-14 20:03:53,874 DEBUG quick_run starting in: /home/data/HI1602/proc/os75bb 2015-11-14 20:03:53,874 DEBUG quick_run executing commands from: edit 2015-11-14 20:03:53,875 DEBUG quick_run about to run dbupdate ../adcpdb/a_hi abadprf_tmp.asc 2015-11-14 20:03:53,879 DEBUG quick_run about to run badbin ../adcpdb/a_hi abadbin_tmp.asc 2015-11-14 20:03:53,885 DEBUG quick_subs dbname: ../adcpdb/a_hi pg_min: 50 set_range_bit time_ranges: all 2015-11-14 20:03:53,885 DEBUG quick_run about to run setflags setflags.tmp 2015-11-14 20:03:53,929 DEBUG quick_run changing directories back to /home/data/HI1602/proc/os75bb 2015-11-14 20:03:53,929 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:53,929 INFO quick_adcp step 12: run calibration steps 2015-11-14 20:03:53,929 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2015-11-14 20:03:53,929 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:53,930 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/cal/botmtrk 2015-11-14 20:03:53,930 DEBUG quick_setup running python command "lst_btrk" 2015-11-14 20:03:53,930 DEBUG quick_subs dbname: ../../adcpdb/a_hi output: a_hi.btm step_size= 1 year_base= 2015 time_ranges: 2015/11/01 19:23:48 to 2015/11/14 19:58:49 /* whole time range */ 2015-11-14 20:03:53,930 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2015-11-14 20:03:53,946 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2015-11-14 20:03:53,946 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:53,946 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/cal/botmtrk 2015-11-14 20:03:53,946 DEBUG quick_setup running python command "refabsbt" 2015-11-14 20:03:53,946 DEBUG quick_subs fix_file_type: simple reference_file: a_hi.btm fix_file: ../../nav/a_hi.gps output: a_hi.ref year_base= 2015 ensemble_length= 300 gap_tolerance= 60 2015-11-14 20:03:53,946 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2015-11-14 20:03:53,951 INFO quick_run ...bottom track info in check cal/botmtrk 2015-11-14 20:03:53,951 DEBUG quick_mpl Starting plot: btcal 2015-11-14 20:03:53,952 DEBUG quick_mpl No data in a_hi.btm 2015-11-14 20:03:53,952 DEBUG quick_mpl Returning from Btplot with no output 2015-11-14 20:03:53,952 DEBUG quick_mpl Ending plot: btcal 2015-11-14 20:03:53,952 DEBUG quick_setup nav/as_nav.tmp exists 2015-11-14 20:03:53,952 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:53,952 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/nav 2015-11-14 20:03:53,952 DEBUG quick_setup running python command "as_nav" 2015-11-14 20:03:53,952 DEBUG quick_subs dbname: ../adcpdb/a_hi output: a_hi step_size: 1 ndepth: 20 time_ranges: separate year_base= 2015 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 2015/11/01 19:23:48 to 2015/11/14 19:58:49 /* the whole time range */ 2015-11-14 20:03:53,952 DEBUG quick_setup about to run adcpsect as_nav.tmp 2015-11-14 20:03:54,010 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2015-11-14 20:03:54,010 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:54,010 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/cal/watertrk 2015-11-14 20:03:54,010 DEBUG quick_setup running python command "timslip" 2015-11-14 20:03:54,010 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_hi.gps reference_file: ../../nav/a_hi.nav output_file: a_hi_7.cal year_base= 2015 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 2015-11-14 20:03:54,010 DEBUG quick_setup about to run timslip timslip.tmp 2015-11-14 20:03:54,024 INFO quick_run ... watertrack info in cal/watertrk 2015-11-14 20:03:54,025 DEBUG quick_mpl Starting plot: wtcal 2015-11-14 20:03:54,026 DEBUG quick_mpl Found 34 calibration points 2015-11-14 20:03:55,382 DEBUG quick_mpl Ending plot: wtcal 2015-11-14 20:03:55,383 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:55,383 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/cal/watertrk 2015-11-14 20:03:55,383 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2015-11-14 20:03:55,383 DEBUG quick_npy Starting: guess_xducerxy 2015-11-14 20:03:55,520 DEBUG quick_npy Ending: guess_xducerxy 2015-11-14 20:03:55,520 INFO quick_run ... check cal/watertrk for estimate 2015-11-14 20:03:55,520 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:55,520 INFO quick_adcp step 13: extract and plot temperature 2015-11-14 20:03:55,520 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:55,521 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/edit 2015-11-14 20:03:55,521 DEBUG quick_setup running python command "lst_temp" 2015-11-14 20:03:55,521 DEBUG quick_subs dbname: ../adcpdb/a_hi output: a_hi.tem step_size= 1 year_base= 2015 time_ranges: all 2015-11-14 20:03:55,521 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2015-11-14 20:03:55,553 DEBUG quick_mpl Starting plot: temp 2015-11-14 20:03:55,587 DEBUG quick_mpl plotting 3752 points 2015-11-14 20:03:56,024 DEBUG quick_mpl Ending plot: temp 2015-11-14 20:03:56,024 INFO quick_run plotted temperature 2015-11-14 20:03:56,025 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:56,025 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2015-11-14 20:03:56,025 DEBUG quick_setup edit/lst_npings.tmp exists 2015-11-14 20:03:56,025 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:56,025 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/edit 2015-11-14 20:03:56,026 DEBUG quick_setup running python command "lst_npings" 2015-11-14 20:03:56,026 DEBUG quick_subs dbname: ../adcpdb/a_hi output: a_hi_npings.txt step_size= 1 year_base= 2015 time_ranges: all 2015-11-14 20:03:56,026 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2015-11-14 20:03:56,081 DEBUG quick_mpl Starting plot: npings 2015-11-14 20:03:56,136 DEBUG quick_mpl plotting 3752 points 2015-11-14 20:03:56,429 DEBUG quick_mpl Ending plot: npings 2015-11-14 20:03:56,430 INFO quick_run ... plotted number of pings per ensemble 2015-11-14 20:03:56,430 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:56,430 INFO quick_adcp step 15: extract matlab "allbins" 2015-11-14 20:03:56,430 DEBUG quick_asect step 18: make matlab files for plotting 2015-11-14 20:03:56,431 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:56,431 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/vector 2015-11-14 20:03:56,431 DEBUG quick_setup running python command "timegrid" 2015-11-14 20:03:56,431 DEBUG quick_setup about to run timegrid a_hi.tmp 2015-11-14 20:03:56,448 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:56,449 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/vector 2015-11-14 20:03:56,449 DEBUG quick_setup running python command "as_vect" 2015-11-14 20:03:56,450 DEBUG quick_setup about to run adcpsect as_vect.tmp 2015-11-14 20:03:56,574 DEBUG quick_asect done making vector matfiles 2015-11-14 20:03:56,575 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:56,575 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/contour 2015-11-14 20:03:56,575 DEBUG quick_setup running python command "timegrid" 2015-11-14 20:03:56,576 DEBUG quick_setup about to run timegrid a_hi.tmp 2015-11-14 20:03:56,587 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:56,587 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/contour 2015-11-14 20:03:56,587 DEBUG quick_setup running python command "as_cont" 2015-11-14 20:03:56,588 DEBUG quick_setup about to run adcpsect as_cont.tmp 2015-11-14 20:03:56,756 DEBUG quick_setup starting in /home/data/HI1602/proc/os75bb 2015-11-14 20:03:56,756 DEBUG quick_setup executing commands from /home/data/HI1602/proc/os75bb/contour 2015-11-14 20:03:56,757 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_hi 2015-11-14 20:03:57,677 DEBUG quick_asect done running getmat with "allbins" 2015-11-14 20:03:57,678 INFO quick_adcp --------------------------------------------- 2015-11-14 20:03:57,678 INFO quick_adcp writing "cruise_info.txt" 2015-11-14 20:03:57,684 INFO root copying NOFIG to /home/adcp/www/figures/os75bb_hcorr_plot.png 2015-11-14 20:03:57,684 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os75bb_hcorr_plot_thumb.png 2015-11-14 20:03:57,685 DEBUG root matfile is contour/contour_uv.mat 2015-11-14 20:03:57,690 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os75bb_cont_uv.mat 2015-11-14 20:03:57,690 DEBUG root matfile is vector/vector_uv.mat 2015-11-14 20:03:57,691 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os75bb_vect_uv.mat 2015-11-14 20:03:57,691 DEBUG root matfile is contour/contour_xy.mat 2015-11-14 20:03:57,692 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os75bb_cont_xy.mat 2015-11-14 20:03:57,692 DEBUG root matfile is vector/vector_xy.mat 2015-11-14 20:03:57,693 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os75bb_vect_xy.mat 2015-11-14 20:03:57,693 DEBUG root about to copy file edit/a_hi.tem to /home/adcp/www/data/os75bb_temp.asc 2015-11-14 20:03:57,694 INFO root copying edit/a_hi.tem to /home/adcp/www/data/os75bb_temp.asc 2015-11-14 20:03:57,709 INFO netcdf Using pupynere. 2015-11-14 20:03:58,031 DEBUG root about to copy netcdf file /home/data/HI1602/proc/os75bb/contour/os75bb.nc to /home/adcp/www/data/os75bb.nc 2015-11-14 20:03:58,048 INFO root copying edit/a_hi.tem to /home/adcp/www/data/os75bb.nc 2015-11-14 20:03:58,113 INFO root generating pingstats for os75bb 2015-11-14 20:03:58,113 INFO root Ending quick_adcp.py