2018-06-24 18:50:49,396 DEBUG root about to write control file parameters to --yearbase 2018 --cruisename SR1808 --configtype python --sonar os38nb --dbname a_sr --datatype uhdas --cfgpath /home/data/SR1808/proc/os38nb/config --ens_len 300 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea #offset between transducer and gps, applied in at-sea processing # NOTE : read special instructions to change offsets # diagnostics in cal/watertrk/guess_xducerxy.out # parameters used: --xducer_dx -6 --xducer_dy 11 ## see config/SR1808_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 2018-06-24 18:50:49,450 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d os38nb 2018-06-24 18:50:49,454 DEBUG quick_setup found cruise_info.hcorr (seapath, sea, 0) 2018-06-24 18:50:49,454 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2018-06-24 18:50:49,454 INFO quick_setup fix file is a_sr.gps 2018-06-24 18:50:49,455 INFO quick_setup reflayer: ref_method = refsm 2018-06-24 18:50:49,455 INFO quick_setup reflayer: refuv_source = nav 2018-06-24 18:50:49,455 INFO quick_setup reflayer: refuv_smoothwin = 3 2018-06-24 18:50:49,455 INFO quick_adcp importing numpy version 1.11.0 2018-06-24 18:50:49,477 INFO quick_adcp importing matplotlib version 1.5.1 2018-06-24 18:50:49,646 DEBUG quick_mpl in Q_mpl 2018-06-24 18:50:49,646 INFO quick_adcp ===================================================== 2018-06-24 18:50:49,646 INFO quick_adcp ===================================================== 2018-06-24 18:50:49,646 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d os38nb 2018-06-24 18:50:49,646 INFO quick_adcp cwd is /mnt/md0/data/SR1808/proc/os38nb about to run these steps: - write_clearflags - scandata - avg_and_load - codaseditsetup - setflags - getnav - lst_hdg - plot_headcorr - navsteps - find_pflags - apply_edit - navsteps - lst_temp - plot_temp - lst_npings - calib - matfiles - adcpsect - refabs - smoothnav - putnav - refplots - find_pflags - codaseditsetup 2018-06-24 18:50:49,646 DEBUG quick_asect extracting matlab files for os38nb 2018-06-24 18:50:49,656 DEBUG quick_setup data directory: /home/data/SR1808/raw/os38 2018-06-24 18:50:49,657 INFO quick_setup found 183 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/SR1808/raw/os38/*.raw" 2018-06-24 18:50:49,766 INFO quick_setup presently in scan, writing filelist to /mnt/md0/data/SR1808/proc/os38nb/ping/datafile_list.txt 2018-06-24 18:50:49,767 INFO quick_setup found 183 raw data files 2018-06-24 18:50:49,768 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/SR1808/raw/os38/sr2018_159_56259.raw ... 2018-06-24 18:50:49,769 DEBUG quick_adcp Sun Jun 24 18:50:49 2018 running quick_adcp.py as follows: --cntfile /home/data/SR1808/proc/os38nb/os38nb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_sr dbpath ../adcpdb deeper_boundaries [100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600] firstdepth 43 gridnum 80 increment 20 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2018 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/SR1808/proc/os38nb/config cntfile /home/data/SR1808/proc/os38nb/os38nb_qpy.cnt commands None configtype python cruisename SR1808 data_def vmadcp.def data_filelist /mnt/md0/data/SR1808/proc/os38nb/ping/datafile_list.txt datadir /home/data/SR1808/raw/os38 datafile_glob *.raw datatype uhdas dbname a_sr dday_bailout 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'/home/data/SR1808/raw/os38/sr2018_173_64800.raw', '/home/data/SR1808/raw/os38/sr2018_173_72000.raw', '/home/data/SR1808/raw/os38/sr2018_173_79200.raw', '/home/data/SR1808/raw/os38/sr2018_174_00000.raw', '/home/data/SR1808/raw/os38/sr2018_174_07200.raw', '/home/data/SR1808/raw/os38/sr2018_174_14400.raw', '/home/data/SR1808/raw/os38/sr2018_174_21600.raw', '/home/data/SR1808/raw/os38/sr2018_174_28800.raw', '/home/data/SR1808/raw/os38/sr2018_174_36000.raw', '/home/data/SR1808/raw/os38/sr2018_174_43200.raw', '/home/data/SR1808/raw/os38/sr2018_174_50400.raw', '/home/data/SR1808/raw/os38/sr2018_174_57600.raw', '/home/data/SR1808/raw/os38/sr2018_174_64800.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 43 fixfile a_sr.gps fixfilexy a_sr.agt frequency 38 hcorr_inst seapath help False incremental True instname os38 jitter 15 max_BLKprofiles 300 max_search_depth 2000 maxrunsecs None min_filter_fraction 0.5 mixed_pings False model os nosave_editcfg 0 numbins 128 pgmin 50 ping_headcorr True pingpref None pingtype nb printformats png proc_engine python proc_yearbase 2018 procdir /mnt/md0/data/SR1808/proc/os38nb py_gbindirbase /home/data/SR1808/gbin ref_method refsm refuv_inputfile a_sr.agt refuv_smoothwin 3 refuv_source nav rl_endbin 20 rl_startbin 2 rotate_amplitude 1 rotate_angle 0 save_lastens 0 skip_avg True sonar os38nb steps2rerun sum_xducer_dx -6 sum_xducer_dy 11 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_sr.agt ub_type 1920 uhdas_config yearbase = 2018 uhdas_dir = /home/data/SR1808 sonar = os38nb gbin = /home/data/SR1808/gbin gbinsonar = /home/data/SR1808/gbin/os38 raw = /home/data/SR1808/raw rawsonar = /home/data/SR1808/raw/os38 rbin = /home/data/SR1808/rbin proc = /home/data/SR1808/proc procsonar = /home/data/SR1808/proc/os38nb other attributes: gbin_params = hdg_inst : hydrins hdg_inst_msgs : [('hydrins', 'hdg'), ('seapath', 'sea'), ('trimble', 'hdg'), ('hemisphere', 'hdg')] hdg_msg : hdg pitch_inst : seapath pitch_msg : sea pos_inst : trimble pos_msg : gps roll_inst : seapath roll_msg : sea hcorr = ['seapath', 'sea', 0.0] acc_heading_cutoff = 0.02 update_gbin False uvwref_end None uvwref_start None vardoc False varvals False wtrk_step 7 xducer_dx -6 xducer_dy 11 yearbase 2018 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 2018-06-24 18:50:49,769 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:49,769 INFO quick_adcp step 1: set up files in "edit" directory 2018-06-24 18:50:49,769 INFO quick_run file exists (edit/clearflags.tmp). not writing 2018-06-24 18:50:49,770 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:49,770 INFO quick_adcp step 2: scan files for time range 2018-06-24 18:50:49,770 DEBUG quick_npy Starting: scanping 2018-06-24 18:50:49,866 DEBUG quick_npy Ending: scanping 2018-06-24 18:50:49,866 DEBUG quick_subs start_end_time 2018/06/09 15:37:42 to 2018/06/09 15:42:54 2018-06-24 18:50:49,866 DEBUG quick_subs dd0: 159.651181 dd1: 159.654792 2018-06-24 18:50:49,866 INFO quick_adcp looking for database with adcpdb/a_sr*.blk 2018-06-24 18:50:49,867 INFO quick_adcp database found: listing blocks 2018-06-24 18:50:49,867 DEBUG quick_subs removing a_srdir.blk 2018-06-24 18:50:49,867 DEBUG quick_subs about to run mkblkdir 2018-06-24 18:50:49,867 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-06-24 18:50:49,867 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-06-24 18:50:49,874 DEBUG quick_subs database passes. 2018-06-24 18:50:49,874 DEBUG quick_subs start_end_time 2018/06/09 15:42:39 to 2018/06/24 18:42:41 2018-06-24 18:50:49,874 DEBUG quick_subs dd0: 159.654618 dd1: 174.779641 2018-06-24 18:50:49,874 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2018-06-24 18:50:49,874 DEBUG quick_adcp origdb_time_range is 2018/06/09 15:42:39 to 2018/06/24 18:42:41 2018-06-24 18:50:49,874 DEBUG quick_adcp (159.654618 to 174.779641) 2018-06-24 18:50:49,875 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:49,875 INFO quick_adcp step 3: generate averaged data... 2018-06-24 18:50:49,875 INFO quick_run file load/ping_editparams.txt exists. not replacing 2018-06-24 18:50:49,875 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:49,875 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/load 2018-06-24 18:50:49,875 DEBUG quick_setup running python command "run_pingavg_npy" 2018-06-24 18:50:49,875 DEBUG quick_npy Starting: pingavg 2018-06-24 18:50:49,876 DEBUG quick_npy xducerxy is [-6, 11] 2018-06-24 18:50:49,876 DEBUG quick_npy uvwref is None 2018-06-24 18:50:49,876 DEBUG quick_npy singleping editing parameters: 2018-06-24 18:50:49,876 DEBUG quick_npy bigtarget_mab_window : 11 2018-06-24 18:50:49,876 DEBUG quick_npy rl_endbin : 20 2018-06-24 18:50:49,876 DEBUG quick_npy max_search_depth : 2000 2018-06-24 18:50:49,877 DEBUG quick_npy cor_cutoff : 120 2018-06-24 18:50:49,877 DEBUG quick_npy ampfilt : 40 2018-06-24 18:50:49,877 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2018-06-24 18:50:49,877 DEBUG quick_npy rl_startbin : 2 2018-06-24 18:50:49,877 DEBUG quick_npy ecutoff : 0.800000 2018-06-24 18:50:49,877 DEBUG quick_npy refavg_valcutoff : 1 2018-06-24 18:50:49,877 DEBUG quick_npy weakprof_percent : 30 2018-06-24 18:50:49,877 DEBUG quick_npy bigtarget_ampthresh : 55 2018-06-24 18:50:49,880 INFO pingavg ---------------- 2018-06-24 18:50:49,880 INFO pingavg sonar is os38nb 2018-06-24 18:50:49,880 INFO pingavg Pingavg.run for time range 174.750020 to 174.783318 2018-06-24 18:50:49,881 INFO pingavg transducer offset: xducer_dx = -6.000, xducer_dy = 11.000 2018-06-24 18:50:49,881 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2018-06-24 18:50:49,881 INFO pingavg ---------------- 2018-06-24 18:50:49,890 DEBUG pingavg Chunk 1 of 1, 174.750020 to 174.783318 2018-06-24 18:50:49,890 DEBUG pingavg Nothing written 2018-06-24 18:50:49,890 DEBUG quick_npy wrote 0 averages 2018-06-24 18:50:49,890 DEBUG quick_npy Ending: pingavg 2018-06-24 18:50:49,890 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:49,890 INFO quick_adcp step 4: load averaged data (to database) 2018-06-24 18:50:49,891 DEBUG quick_subs in del_overlapping 2018-06-24 18:50:49,891 DEBUG quick_subs lastblock: 2018-06-24 18:50:49,891 DEBUG quick_subs 15 2018-06-24 18:50:49,891 DEBUG quick_subs lastcmd: 2018-06-24 18:50:49,891 DEBUG quick_subs 15 2018-06-24 18:50:49,891 DEBUG quick_subs delblks: 2018-06-24 18:50:49,891 DEBUG quick_subs [15] 2018-06-24 18:50:49,891 DEBUG quick_subs loadblks: 2018-06-24 18:50:49,891 DEBUG quick_subs [15] 2018-06-24 18:50:49,891 DEBUG quick_subs about to run mkblkdir 2018-06-24 18:50:49,891 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-06-24 18:50:49,891 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-06-24 18:50:49,898 DEBUG quick_subs database passes. 2018-06-24 18:50:49,898 DEBUG quick_subs start_end_time 2018/06/09 15:42:39 to 2018/06/24 05:37:39 2018-06-24 18:50:49,898 DEBUG quick_subs dd0: 159.654618 dd1: 174.234479 2018-06-24 18:50:49,898 DEBUG quick_run [15] 2018-06-24 18:50:49,898 DEBUG quick_run cmdlist 2018-06-24 18:50:49,898 DEBUG quick_run ['./ens_blk015.cmd'] 2018-06-24 18:50:49,899 INFO quick_run loaded time range: 2018/06/24 05:42:39 to 2018/06/24 18:47:41 2018-06-24 18:50:49,899 DEBUG quick_setup load/ldcodas.tmp exists 2018-06-24 18:50:49,899 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:49,899 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/load 2018-06-24 18:50:49,899 DEBUG quick_setup running python command "ldcodas" 2018-06-24 18:50:49,899 DEBUG quick_subs filling "thisload" timerange 2018-06-24 18:50:49,900 DEBUG quick_subs in ldcodas 2018-06-24 18:50:49,900 DEBUG quick_subs cmdlist: 2018-06-24 18:50:49,900 DEBUG quick_subs ['./ens_blk015.cmd'] 2018-06-24 18:50:49,900 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_sr DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2018 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk015.cmd 2018-06-24 18:50:49,900 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2018-06-24 18:50:49,916 INFO quick_run 16 block files present 2018-06-24 18:50:49,916 DEBUG quick_subs removing a_srdir.blk 2018-06-24 18:50:49,916 DEBUG quick_subs about to run mkblkdir 2018-06-24 18:50:49,916 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-06-24 18:50:49,916 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-06-24 18:50:49,922 DEBUG quick_subs database passes. 2018-06-24 18:50:49,923 DEBUG quick_subs start_end_time 2018/06/09 15:42:39 to 2018/06/24 18:47:41 2018-06-24 18:50:49,923 DEBUG quick_subs dd0: 159.654618 dd1: 174.783113 2018-06-24 18:50:49,923 INFO quick_adcp database time range: 2018-06-24 18:50:49,923 INFO quick_adcp 2018/06/09 15:42:39 to 2018/06/24 18:47:41 2018-06-24 18:50:49,923 INFO quick_adcp (159.654618 to 174.783113) 2018-06-24 18:50:49,923 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:49,923 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/adcpdb 2018-06-24 18:50:49,923 DEBUG quick_setup running python command "lst_conf" 2018-06-24 18:50:49,923 DEBUG quick_subs dbname: a_sr output: a_sr.cnh time_ranges: all 2018-06-24 18:50:49,923 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2018-06-24 18:50:49,936 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:49,937 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2018-06-24 18:50:49,937 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2018-06-24 18:50:49,937 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:49,937 INFO quick_adcp step 6: run setflags? 2018-06-24 18:50:49,937 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:49,937 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/edit 2018-06-24 18:50:49,937 DEBUG quick_setup running python command "write_setflags" 2018-06-24 18:50:49,937 DEBUG quick_subs dbname: ../adcpdb/a_sr pg_min: 50 set_range_bit time_ranges: all 2018-06-24 18:50:49,937 DEBUG quick_setup about to run setflags setflags.tmp 2018-06-24 18:50:49,966 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:49,966 INFO quick_adcp step 7: get navigation 2018-06-24 18:50:49,966 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:49,966 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/nav 2018-06-24 18:50:49,966 DEBUG quick_setup running python command "catnav" 2018-06-24 18:50:49,967 INFO quick_subs navigation file nav/a_sr.gps created from load/*.gps2 2018-06-24 18:50:49,968 INFO quick_subs navigation file nav/a_sr.agt created from load/*.gpst2 2018-06-24 18:50:49,969 DEBUG quick_mpl Starting plot: uvship 2018-06-24 18:50:50,320 DEBUG quick_mpl Ending plot: uvship 2018-06-24 18:50:50,320 INFO quick_run plotted uvship 2018-06-24 18:50:50,320 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:50,320 INFO quick_adcp step 8: list heading 2018-06-24 18:50:50,320 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2018-06-24 18:50:50,320 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:50,320 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/cal/rotate 2018-06-24 18:50:50,320 DEBUG quick_setup running python command "lst_hdg" 2018-06-24 18:50:50,320 DEBUG quick_subs dbname: ../../adcpdb/a_sr output: scn.hdg step_size= 1 year_base= 2018 time_ranges: all 2018-06-24 18:50:50,395 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2018-06-24 18:50:50,436 INFO quick_run ... headings extracted 2018-06-24 18:50:50,437 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:50,437 INFO quick_adcp step 9: plot heading correction 2018-06-24 18:50:50,437 DEBUG quick_run hcorr_inst is seapath 2018-06-24 18:50:50,437 DEBUG quick_mpl Starting plot: hcorr 2018-06-24 18:50:50,488 DEBUG quick_mpl found 15.128488 days of data 2018-06-24 18:50:50,488 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2018-06-24 18:50:50,488 DEBUG quick_mpl printing 4 pages 2018-06-24 18:50:51,075 DEBUG quick_mpl Ending plot: hcorr 2018-06-24 18:50:51,076 INFO quick_run plots are in cal/rotate/*png 2018-06-24 18:50:51,076 INFO quick_adcp ------------------------- 2018-06-24 18:50:51,076 INFO quick_adcp ---- running navsteps --- 2018-06-24 18:50:51,076 INFO quick_adcp ------------------------- 2018-06-24 18:50:51,076 INFO quick_adcp step 10: nav steps: run adcpsect 2018-06-24 18:50:51,076 INFO quick_adcp navstep 1 2018-06-24 18:50:51,076 DEBUG quick_setup nav/as_nav.tmp exists 2018-06-24 18:50:51,076 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:51,076 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/nav 2018-06-24 18:50:51,076 DEBUG quick_setup running python command "as_nav" 2018-06-24 18:50:51,076 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2018 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 2018/06/09 15:42:39 to 2018/06/24 18:47:41 /* the whole time range */ 2018-06-24 18:50:51,076 DEBUG quick_setup about to run adcpsect as_nav.tmp 2018-06-24 18:50:51,116 INFO quick_run ... ran adcpsect for navsteps 2018-06-24 18:50:51,116 INFO quick_adcp ------------------------- 2018-06-24 18:50:51,116 INFO quick_adcp step 11: nav steps: run refabs 2018-06-24 18:50:51,116 INFO quick_adcp navstep 2 2018-06-24 18:50:51,116 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:51,116 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/nav 2018-06-24 18:50:51,116 DEBUG quick_setup running python command "refabs" 2018-06-24 18:50:51,116 DEBUG quick_subs fix_file_type: simple reference_file: a_sr.nav fix_file: a_sr.agt output: a_sr.ref year_base= 2018 ensemble_length= 300 gap_tolerance= 10 2018-06-24 18:50:51,116 DEBUG quick_setup about to run refabs refabs.tmp 2018-06-24 18:50:51,140 INFO quick_run ... ran refabs for navsteps 2018-06-24 18:50:51,140 INFO quick_adcp ------------------------- 2018-06-24 18:50:51,140 INFO quick_adcp step 12: nav steps: run smoothr for plots 2018-06-24 18:50:51,140 INFO quick_adcp navstep 3 2018-06-24 18:50:51,140 DEBUG quick_setup nav/smoothr.tmp exists 2018-06-24 18:50:51,140 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:51,141 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/nav 2018-06-24 18:50:51,141 DEBUG quick_setup running python command "smoothr" 2018-06-24 18:50:51,141 DEBUG quick_subs reference_file: a_sr.nav refabs_output: a_sr.ref output: a_sr.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 2018-06-24 18:50:51,141 DEBUG quick_setup about to run smoothr smoothr.tmp 2018-06-24 18:50:51,253 INFO quick_run ... ran smoothr 2018-06-24 18:50:51,254 INFO quick_adcp ------------------------- 2018-06-24 18:50:51,254 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2018-06-24 18:50:51,254 INFO quick_adcp navstep 4 2018-06-24 18:50:51,254 INFO quick_run smoothing method for ship speed: refsm 2018-06-24 18:50:51,254 INFO quick_run smoothing window: 3 2018-06-24 18:50:51,254 INFO quick_run ship speed source: nav 2018-06-24 18:50:51,254 DEBUG quick_npy Starting: refsm 2018-06-24 18:50:51,413 DEBUG quick_npy Ending: refsm 2018-06-24 18:50:51,413 INFO quick_run ... shipspeed smoothing step done 2018-06-24 18:50:51,413 INFO quick_adcp ------------------------- 2018-06-24 18:50:51,413 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2018-06-24 18:50:51,413 INFO quick_adcp navstep 5 2018-06-24 18:50:51,414 DEBUG quick_setup nav/put_txy.tmp exists 2018-06-24 18:50:51,414 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:51,414 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/nav 2018-06-24 18:50:51,414 DEBUG quick_setup running python command "put_txy" 2018-06-24 18:50:51,414 DEBUG quick_subs dbname: ../adcpdb/a_sr position_file: a_sr.agt year_base= 2018 tolerance= 5 2018-06-24 18:50:51,414 DEBUG quick_setup about to run put_txy put_txy.tmp 2018-06-24 18:50:51,438 INFO quick_run ... ran put_txy 2018-06-24 18:50:51,438 DEBUG quick_setup nav/put_tuv.tmp exists 2018-06-24 18:50:51,438 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:51,438 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/nav 2018-06-24 18:50:51,438 DEBUG quick_setup running python command "put_tuv" 2018-06-24 18:50:51,438 DEBUG quick_subs dbname: ../adcpdb/a_sr shipspeed_file: refsm_tuv.asc year_base= 2018 tolerance= 5 2018-06-24 18:50:51,438 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2018-06-24 18:50:51,461 INFO quick_run ... ran put_tuv 2018-06-24 18:50:51,461 DEBUG quick_mpl Starting plot: nav 2018-06-24 18:50:51,675 DEBUG quick_mpl Ending plot: nav 2018-06-24 18:50:51,675 INFO quick_run ... made navigation plot 2018-06-24 18:50:51,675 INFO quick_adcp ------------------------- 2018-06-24 18:50:51,675 INFO quick_adcp step 15: nav steps: make reflayer plots 2018-06-24 18:50:51,675 INFO quick_adcp navstep 6 2018-06-24 18:50:51,675 DEBUG quick_mpl Starting plot: refl 2018-06-24 18:50:51,738 DEBUG quick_mpl found 15.107621 days of data 2018-06-24 18:50:51,738 DEBUG quick_mpl start day is 159.000000 2018-06-24 18:50:51,738 DEBUG quick_mpl figures with 2.000000 days per page 2018-06-24 18:50:51,738 DEBUG quick_mpl printing 8 pages 2018-06-24 18:50:51,738 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2018-06-24 18:50:52,334 DEBUG quick_mpl Ending plot: refl 2018-06-24 18:50:52,334 INFO quick_run ... made reflayer plots 2018-06-24 18:50:52,334 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:52,334 INFO quick_adcp step 10: find profile flags 2018-06-24 18:50:52,335 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:52,335 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/edit 2018-06-24 18:50:52,335 DEBUG quick_setup running python command "run_autoedit_npy" 2018-06-24 18:50:52,335 DEBUG quick_npy Starting: autoedit 2018-06-24 18:50:52,490 DEBUG pingedit wrote 57 bad bins to abadbin_tmp.asc 2018-06-24 18:50:52,495 DEBUG pingedit wrote 53 bad profiles to abadprf_tmp.asc 2018-06-24 18:50:52,495 DEBUG quick_npy Ending: autoedit 2018-06-24 18:50:52,495 INFO quick_run ... extracted files using automatic editing 2018-06-24 18:50:52,495 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:52,495 INFO quick_adcp step 11: apply editing 2018-06-24 18:50:52,495 DEBUG quick_run starting in: /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:52,495 DEBUG quick_run executing commands from: edit 2018-06-24 18:50:52,496 DEBUG quick_run about to run dbupdate ../adcpdb/a_sr abadprf_tmp.asc 2018-06-24 18:50:52,501 DEBUG quick_run about to run badbin ../adcpdb/a_sr abadbin_tmp.asc 2018-06-24 18:50:52,508 DEBUG quick_subs dbname: ../adcpdb/a_sr pg_min: 50 set_range_bit time_ranges: all 2018-06-24 18:50:52,508 DEBUG quick_run about to run setflags setflags.tmp 2018-06-24 18:50:52,542 DEBUG quick_run changing directories back to /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:52,543 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:52,543 INFO quick_adcp step 12: run calibration steps 2018-06-24 18:50:52,543 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2018-06-24 18:50:52,543 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:52,543 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/cal/botmtrk 2018-06-24 18:50:52,543 DEBUG quick_setup running python command "lst_btrk" 2018-06-24 18:50:52,543 DEBUG quick_subs dbname: ../../adcpdb/a_sr output: a_sr.btm step_size= 1 year_base= 2018 time_ranges: 2018/06/09 15:42:39 to 2018/06/24 18:47:41 /* whole time range */ 2018-06-24 18:50:52,543 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2018-06-24 18:50:52,556 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2018-06-24 18:50:52,557 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:52,557 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/cal/botmtrk 2018-06-24 18:50:52,557 DEBUG quick_setup running python command "refabsbt" 2018-06-24 18:50:52,557 DEBUG quick_subs fix_file_type: simple reference_file: a_sr.btm fix_file: ../../nav/a_sr.agt output: a_sr.ref year_base= 2018 ensemble_length= 300 gap_tolerance= 60 2018-06-24 18:50:52,557 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2018-06-24 18:50:52,563 INFO quick_run ...bottom track info in check cal/botmtrk 2018-06-24 18:50:52,563 DEBUG quick_mpl Starting plot: btcal 2018-06-24 18:50:52,564 DEBUG quick_mpl No data in a_sr.btm 2018-06-24 18:50:52,564 DEBUG quick_mpl Returning from Btplot with no output 2018-06-24 18:50:52,564 DEBUG quick_mpl Ending plot: btcal 2018-06-24 18:50:52,564 DEBUG quick_setup nav/as_nav.tmp exists 2018-06-24 18:50:52,564 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:52,564 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/nav 2018-06-24 18:50:52,564 DEBUG quick_setup running python command "as_nav" 2018-06-24 18:50:52,564 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2018 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 2018/06/09 15:42:39 to 2018/06/24 18:47:41 /* the whole time range */ 2018-06-24 18:50:52,564 DEBUG quick_setup about to run adcpsect as_nav.tmp 2018-06-24 18:50:52,602 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2018-06-24 18:50:52,602 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:52,602 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/cal/watertrk 2018-06-24 18:50:52,602 DEBUG quick_setup running python command "timslip" 2018-06-24 18:50:52,602 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_sr.agt reference_file: ../../nav/a_sr.nav output_file: a_sr_7.cal year_base= 2018 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 2018-06-24 18:50:52,602 DEBUG quick_setup about to run timslip timslip.tmp 2018-06-24 18:50:52,615 INFO quick_run ... watertrack info in cal/watertrk 2018-06-24 18:50:52,616 DEBUG quick_mpl Starting plot: wtcal 2018-06-24 18:50:52,618 DEBUG quick_mpl Found 116 calibration points 2018-06-24 18:50:53,308 DEBUG quick_mpl Ending plot: wtcal 2018-06-24 18:50:53,308 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:53,308 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/cal/watertrk 2018-06-24 18:50:53,309 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2018-06-24 18:50:53,309 DEBUG quick_npy Starting: guess_xducerxy 2018-06-24 18:50:53,437 DEBUG quick_npy Ending: guess_xducerxy 2018-06-24 18:50:53,437 INFO quick_run ... check cal/watertrk for estimate 2018-06-24 18:50:53,437 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:53,437 INFO quick_adcp step 13: extract and plot temperature 2018-06-24 18:50:53,438 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:53,438 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/edit 2018-06-24 18:50:53,438 DEBUG quick_setup running python command "lst_temp" 2018-06-24 18:50:53,438 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr.tem step_size= 1 year_base= 2018 time_ranges: all 2018-06-24 18:50:53,438 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2018-06-24 18:50:53,460 DEBUG quick_mpl Starting plot: temp 2018-06-24 18:50:53,484 DEBUG quick_mpl plotting 4358 points 2018-06-24 18:50:53,637 DEBUG quick_mpl Ending plot: temp 2018-06-24 18:50:53,637 INFO quick_run plotted temperature 2018-06-24 18:50:53,637 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:53,637 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2018-06-24 18:50:53,637 DEBUG quick_setup edit/lst_npings.tmp exists 2018-06-24 18:50:53,637 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:53,637 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/edit 2018-06-24 18:50:53,637 DEBUG quick_setup running python command "lst_npings" 2018-06-24 18:50:53,637 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr_npings.txt step_size= 1 year_base= 2018 time_ranges: all 2018-06-24 18:50:53,637 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2018-06-24 18:50:53,656 DEBUG quick_mpl Starting plot: npings 2018-06-24 18:50:53,676 DEBUG quick_mpl plotting 4358 points 2018-06-24 18:50:53,771 DEBUG quick_mpl Ending plot: npings 2018-06-24 18:50:53,771 INFO quick_run ... plotted number of pings per ensemble 2018-06-24 18:50:53,771 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:53,771 INFO quick_adcp step 15: extract matlab "allbins" 2018-06-24 18:50:53,771 DEBUG quick_asect step 18: make matlab files for plotting 2018-06-24 18:50:53,771 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:53,771 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/vector 2018-06-24 18:50:53,772 DEBUG quick_setup running python command "timegrid" 2018-06-24 18:50:53,772 DEBUG quick_setup about to run timegrid a_sr.tmp 2018-06-24 18:50:53,777 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:53,777 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/vector 2018-06-24 18:50:53,777 DEBUG quick_setup running python command "as_vect" 2018-06-24 18:50:53,777 DEBUG quick_setup about to run adcpsect as_vect.tmp 2018-06-24 18:50:53,830 DEBUG quick_asect done making vector matfiles 2018-06-24 18:50:53,830 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:53,830 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/contour 2018-06-24 18:50:53,831 DEBUG quick_setup running python command "timegrid" 2018-06-24 18:50:53,831 DEBUG quick_setup about to run timegrid a_sr.tmp 2018-06-24 18:50:53,837 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:53,837 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/contour 2018-06-24 18:50:53,837 DEBUG quick_setup running python command "as_cont" 2018-06-24 18:50:53,837 DEBUG quick_setup about to run adcpsect as_cont.tmp 2018-06-24 18:50:53,940 DEBUG quick_setup starting in /mnt/md0/data/SR1808/proc/os38nb 2018-06-24 18:50:53,940 DEBUG quick_setup executing commands from /mnt/md0/data/SR1808/proc/os38nb/contour 2018-06-24 18:50:53,940 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_sr 2018-06-24 18:50:54,262 DEBUG quick_asect done running getmat with "allbins" 2018-06-24 18:50:54,262 INFO quick_adcp --------------------------------------------- 2018-06-24 18:50:54,262 INFO quick_adcp writing "cruise_info.txt" 2018-06-24 18:50:54,266 INFO root copying NOFIG to /home/adcp/www/figures/os38nb_hcorr_plot.png 2018-06-24 18:50:54,266 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os38nb_hcorr_plot_thumb.png 2018-06-24 18:50:54,266 DEBUG root matfile is contour/contour_uv.mat 2018-06-24 18:50:54,270 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os38nb_cont_uv.mat 2018-06-24 18:50:54,270 DEBUG root matfile is vector/vector_uv.mat 2018-06-24 18:50:54,271 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os38nb_vect_uv.mat 2018-06-24 18:50:54,271 DEBUG root matfile is contour/contour_xy.mat 2018-06-24 18:50:54,271 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os38nb_cont_xy.mat 2018-06-24 18:50:54,272 DEBUG root matfile is vector/vector_xy.mat 2018-06-24 18:50:54,272 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os38nb_vect_xy.mat 2018-06-24 18:50:54,272 DEBUG root about to copy file edit/a_sr.tem to /home/adcp/www/data/os38nb_temp.asc 2018-06-24 18:50:54,272 INFO root copying edit/a_sr.tem to /home/adcp/www/data/os38nb_temp.asc 2018-06-24 18:50:54,627 DEBUG root about to copy netcdf file /home/data/SR1808/proc/os38nb/contour/os38nb.nc to /home/adcp/www/data/os38nb.nc 2018-06-24 18:50:54,633 INFO root copying /home/data/SR1808/proc/os38nb/contour/os38nb.nc to /home/adcp/www/data/os38nb.nc 2018-06-24 18:50:54,633 INFO root nc_compressed: ddstep is 1 2018-06-24 18:50:54,694 INFO root success: made compressed nc file /home/adcp/uhdas_tmp/os38nb_compr.nc 2018-06-24 18:50:54,726 INFO root generating pingstats for os38nb 2018-06-24 18:50:54,726 INFO root Ending quick_adcp.py