2018-04-13 14:18:12,628 DEBUG root about to write control file parameters to --yearbase 2018 --cruisename RB1802_2 --configtype python --sonar os75nb --dbname a_rb --datatype uhdas --cfgpath /home/data/RB1802_2/proc/os75nb/config --ens_len 300 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea #offset between transducer and gps, applied in at-sea processing # NOTE : read special instructions to change offsets # diagnostics in cal/watertrk/guess_xducerxy.out # parameters used: --xducer_dx -6 --xducer_dy 7 ## see config/RB1802_2_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 2018-04-13 14:18:12,628 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d os75nb 2018-04-13 14:18:12,630 DEBUG quick_setup found cruise_info.hcorr (posmv, pmv, 0) 2018-04-13 14:18:12,630 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2018-04-13 14:18:12,630 INFO quick_setup fix file is a_rb.gps 2018-04-13 14:18:12,631 INFO quick_setup reflayer: ref_method = refsm 2018-04-13 14:18:12,631 INFO quick_setup reflayer: refuv_source = nav 2018-04-13 14:18:12,631 INFO quick_setup reflayer: refuv_smoothwin = 3 2018-04-13 14:18:12,631 INFO quick_adcp importing numpy version 1.8.2 2018-04-13 14:18:12,644 INFO quick_adcp importing matplotlib version 1.4.3 2018-04-13 14:18:12,834 DEBUG quick_mpl in Q_mpl 2018-04-13 14:18:12,834 INFO quick_adcp ===================================================== 2018-04-13 14:18:12,834 INFO quick_adcp ===================================================== 2018-04-13 14:18:12,834 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d os75nb 2018-04-13 14:18:12,834 INFO quick_adcp cwd is /home/data/RB1802_2/proc/os75nb about to run these steps: - write_clearflags - scandata - avg_and_load - codaseditsetup - setflags - getnav - lst_hdg - plot_headcorr - navsteps - find_pflags - apply_edit - navsteps - lst_temp - plot_temp - lst_npings - calib - matfiles - adcpsect - refabs - smoothnav - putnav - refplots - find_pflags - codaseditsetup 2018-04-13 14:18:12,834 DEBUG quick_asect extracting matlab files for os75nb 2018-04-13 14:18:12,838 DEBUG quick_setup data directory: /home/data/RB1802_2/raw/os75 2018-04-13 14:18:12,838 INFO quick_setup found 30 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/RB1802_2/raw/os75/*.raw" 2018-04-13 14:18:12,838 DEBUG quick_setup found 30 files from original filelist 2018-04-13 14:18:12,839 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/RB1802_2/raw/os75/rb2018_100_20869.raw ... 2018-04-13 14:18:12,839 DEBUG quick_adcp Fri Apr 13 14:18:12 2018 running quick_adcp.py as follows: --cntfile /home/data/RB1802_2/proc/os75nb/os75nb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_rb dbpath ../adcpdb deeper_boundaries [50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775] firstdepth 28 gridnum 80 increment 10 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 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/RB1802_2/proc/os75nb/config cntfile /home/data/RB1802_2/proc/os75nb/os75nb_qpy.cnt commands None configtype python cruisename RB1802_2 data_def vmadcp.def datadir /home/data/RB1802_2/raw/os75 datafile_glob *.raw datatype uhdas dbname a_rb dday_bailout None debug False ens_len 300 expert None filelist ['/home/data/RB1802_2/raw/os75/rb2018_100_20869.raw', '/home/data/RB1802_2/raw/os75/rb2018_100_21600.raw', '/home/data/RB1802_2/raw/os75/rb2018_100_28800.raw', '/home/data/RB1802_2/raw/os75/rb2018_100_36000.raw', '/home/data/RB1802_2/raw/os75/rb2018_100_43200.raw', '/home/data/RB1802_2/raw/os75/rb2018_100_50400.raw', '/home/data/RB1802_2/raw/os75/rb2018_100_57600.raw', '/home/data/RB1802_2/raw/os75/rb2018_100_64800.raw', '/home/data/RB1802_2/raw/os75/rb2018_100_72000.raw', '/home/data/RB1802_2/raw/os75/rb2018_100_79200.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_00000.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_07200.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_14400.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_21600.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_28800.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_36000.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_43200.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_50400.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_57600.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_64800.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_72000.raw', '/home/data/RB1802_2/raw/os75/rb2018_101_79200.raw', '/home/data/RB1802_2/raw/os75/rb2018_102_00000.raw', '/home/data/RB1802_2/raw/os75/rb2018_102_07200.raw', '/home/data/RB1802_2/raw/os75/rb2018_102_14400.raw', '/home/data/RB1802_2/raw/os75/rb2018_102_21600.raw', '/home/data/RB1802_2/raw/os75/rb2018_102_28800.raw', '/home/data/RB1802_2/raw/os75/rb2018_102_36000.raw', '/home/data/RB1802_2/raw/os75/rb2018_102_43200.raw', '/home/data/RB1802_2/raw/os75/rb2018_102_50400.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 28 fixfile a_rb.gps fixfilexy a_rb.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 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 py_gbindirbase /home/data/RB1802_2/gbin ref_method refsm refuv_inputfile a_rb.agt refuv_smoothwin 3 refuv_source nav rl_endbin 20 rl_startbin 2 rotate_amplitude 1 rotate_angle 0 save_lastens 0 skip_avg True sonar os75nb steps2rerun sum_xducer_dx -6 sum_xducer_dy 7 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_rb.agt ub_type 1920 uhdas_config yearbase = 2018 uhdas_dir = /home/data/RB1802_2 sonar = os75nb gbin = /home/data/RB1802_2/gbin gbinsonar = /home/data/RB1802_2/gbin/os75 raw = /home/data/RB1802_2/raw rawsonar = /home/data/RB1802_2/raw/os75 rbin = /home/data/RB1802_2/rbin proc = /home/data/RB1802_2/proc procsonar = /home/data/RB1802_2/proc/os75nb other attributes: gbin_params = hdg_inst : gyro hdg_inst_msgs : [('gyro', 'hdg'), ('posmv', 'pmv')] hdg_msg : hdg pitch_inst : posmv pitch_msg : pmv pos_inst : gpsnav pos_msg : gps roll_inst : posmv roll_msg : pmv hcorr = ['posmv', 'pmv', 0] acc_heading_cutoff = 0.02 update_gbin False vardoc False varvals False wtrk_step 7 xducer_dx -6 xducer_dy 7 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 2018-04-13 14:18:12,839 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:12,839 INFO quick_adcp step 1: set up files in "edit" directory 2018-04-13 14:18:12,839 INFO quick_run file exists (edit/clearflags.tmp). not writing 2018-04-13 14:18:12,839 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:12,839 INFO quick_adcp step 2: scan files for time range 2018-04-13 14:18:12,839 DEBUG quick_npy Starting: scanping 2018-04-13 14:18:12,874 DEBUG quick_npy Ending: scanping 2018-04-13 14:18:12,875 DEBUG quick_subs start_end_time 2018/04/11 06:00:01 to 2018/04/11 05:59:57 2018-04-13 14:18:12,875 DEBUG quick_subs dd0: 100.250012 dd1: 100.249965 2018-04-13 14:18:12,875 INFO quick_adcp looking for database with adcpdb/a_rb*.blk 2018-04-13 14:18:12,875 INFO quick_adcp database found: listing blocks 2018-04-13 14:18:12,875 DEBUG quick_subs removing a_rbdir.blk 2018-04-13 14:18:12,876 DEBUG quick_subs about to run mkblkdir 2018-04-13 14:18:12,876 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-04-13 14:18:12,876 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-04-13 14:18:12,883 DEBUG quick_subs database passes. 2018-04-13 14:18:12,884 DEBUG quick_subs start_end_time 2018/04/11 05:52:51 to 2018/04/13 14:02:53 2018-04-13 14:18:12,884 DEBUG quick_subs dd0: 100.245035 dd1: 102.585336 2018-04-13 14:18:12,884 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2018-04-13 14:18:12,884 DEBUG quick_adcp origdb_time_range is 2018/04/11 05:52:51 to 2018/04/13 14:02:53 2018-04-13 14:18:12,884 DEBUG quick_adcp (100.245035 to 102.585336) 2018-04-13 14:18:12,884 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:12,884 INFO quick_adcp step 3: generate averaged data... 2018-04-13 14:18:12,884 INFO quick_run file load/ping_editparams.txt exists. not replacing 2018-04-13 14:18:12,884 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:12,884 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/load 2018-04-13 14:18:12,884 DEBUG quick_setup running python command "run_pingavg_npy" 2018-04-13 14:18:12,885 DEBUG quick_npy Starting: pingavg 2018-04-13 14:18:12,886 DEBUG quick_npy xducerxy is [-6, 7] 2018-04-13 14:18:12,886 DEBUG quick_npy singleping editing parameters: 2018-04-13 14:18:12,886 DEBUG quick_npy bigtarget_mab_window : 11 2018-04-13 14:18:12,887 DEBUG quick_npy rl_endbin : 20 2018-04-13 14:18:12,887 DEBUG quick_npy max_search_depth : 2000 2018-04-13 14:18:12,887 DEBUG quick_npy cor_cutoff : 120 2018-04-13 14:18:12,887 DEBUG quick_npy ampfilt : 40 2018-04-13 14:18:12,887 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2018-04-13 14:18:12,887 DEBUG quick_npy rl_startbin : 2 2018-04-13 14:18:12,887 DEBUG quick_npy ecutoff : 0.800000 2018-04-13 14:18:12,887 DEBUG quick_npy refavg_valcutoff : 1 2018-04-13 14:18:12,887 DEBUG quick_npy weakprof_percent : 30 2018-04-13 14:18:12,887 DEBUG quick_npy bigtarget_ampthresh : 55 2018-04-13 14:18:12,891 INFO pingavg ---------------- 2018-04-13 14:18:12,891 INFO pingavg sonar is os75nb 2018-04-13 14:18:12,891 INFO pingavg Pingavg.run for time range 102.583351 to 102.595878 2018-04-13 14:18:12,891 INFO pingavg transducer offset: xducer_dx = -6.000, xducer_dy = 7.000 2018-04-13 14:18:12,891 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2018-04-13 14:18:12,891 INFO pingavg ---------------- 2018-04-13 14:18:12,917 DEBUG pingavg Chunk 1 of 1, 102.583351 to 102.595878 2018-04-13 14:18:12,917 DEBUG pingavg Nothing written 2018-04-13 14:18:12,917 DEBUG quick_npy wrote 0 averages 2018-04-13 14:18:12,918 DEBUG quick_npy Ending: pingavg 2018-04-13 14:18:12,918 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:12,918 INFO quick_adcp step 4: load averaged data (to database) 2018-04-13 14:18:12,918 DEBUG quick_subs in del_overlapping 2018-04-13 14:18:12,918 DEBUG quick_subs lastblock: 2018-04-13 14:18:12,918 DEBUG quick_subs 3 2018-04-13 14:18:12,918 DEBUG quick_subs lastcmd: 2018-04-13 14:18:12,919 DEBUG quick_subs 3 2018-04-13 14:18:12,919 DEBUG quick_subs delblks: 2018-04-13 14:18:12,919 DEBUG quick_subs [3] 2018-04-13 14:18:12,919 DEBUG quick_subs loadblks: 2018-04-13 14:18:12,919 DEBUG quick_subs [3] 2018-04-13 14:18:12,919 DEBUG quick_subs about to run mkblkdir 2018-04-13 14:18:12,919 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-04-13 14:18:12,919 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-04-13 14:18:12,926 DEBUG quick_subs database passes. 2018-04-13 14:18:12,926 DEBUG quick_subs start_end_time 2018/04/11 05:52:51 to 2018/04/13 07:47:49 2018-04-13 14:18:12,927 DEBUG quick_subs dd0: 100.245035 dd1: 102.324873 2018-04-13 14:18:12,927 DEBUG quick_run [3] 2018-04-13 14:18:12,927 DEBUG quick_run cmdlist 2018-04-13 14:18:12,927 DEBUG quick_run ['./ens_blk003.cmd'] 2018-04-13 14:18:12,928 INFO quick_run loaded time range: 2018/04/13 07:52:49 to 2018/04/13 14:17:52 2018-04-13 14:18:12,928 DEBUG quick_setup load/ldcodas.tmp exists 2018-04-13 14:18:12,928 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:12,928 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/load 2018-04-13 14:18:12,928 DEBUG quick_setup running python command "ldcodas" 2018-04-13 14:18:12,928 DEBUG quick_subs filling "thisload" timerange 2018-04-13 14:18:12,929 DEBUG quick_subs in ldcodas 2018-04-13 14:18:12,929 DEBUG quick_subs cmdlist: 2018-04-13 14:18:12,929 DEBUG quick_subs ['./ens_blk003.cmd'] 2018-04-13 14:18:12,929 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_rb DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2018 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk003.cmd 2018-04-13 14:18:12,929 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2018-04-13 14:18:12,948 INFO quick_run 4 block files present 2018-04-13 14:18:12,949 DEBUG quick_subs removing a_rbdir.blk 2018-04-13 14:18:12,949 DEBUG quick_subs about to run mkblkdir 2018-04-13 14:18:12,949 DEBUG quick_subs database still exists; rerunning mkdirblk 2018-04-13 14:18:12,950 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2018-04-13 14:18:12,963 DEBUG quick_subs database passes. 2018-04-13 14:18:12,963 DEBUG quick_subs start_end_time 2018/04/11 05:52:51 to 2018/04/13 14:17:52 2018-04-13 14:18:12,963 DEBUG quick_subs dd0: 100.245035 dd1: 102.595741 2018-04-13 14:18:12,964 INFO quick_adcp database time range: 2018-04-13 14:18:12,964 INFO quick_adcp 2018/04/11 05:52:51 to 2018/04/13 14:17:52 2018-04-13 14:18:12,964 INFO quick_adcp (100.245035 to 102.595741) 2018-04-13 14:18:12,964 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:12,965 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/adcpdb 2018-04-13 14:18:12,965 DEBUG quick_setup running python command "lst_conf" 2018-04-13 14:18:12,965 DEBUG quick_subs dbname: a_rb output: a_rb.cnh time_ranges: all 2018-04-13 14:18:12,965 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2018-04-13 14:18:12,978 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:12,979 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2018-04-13 14:18:12,979 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2018-04-13 14:18:12,979 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:12,979 INFO quick_adcp step 6: run setflags? 2018-04-13 14:18:12,980 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:12,980 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/edit 2018-04-13 14:18:12,980 DEBUG quick_setup running python command "write_setflags" 2018-04-13 14:18:12,980 DEBUG quick_subs dbname: ../adcpdb/a_rb pg_min: 50 set_range_bit time_ranges: all 2018-04-13 14:18:12,980 DEBUG quick_setup about to run setflags setflags.tmp 2018-04-13 14:18:13,001 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:13,001 INFO quick_adcp step 7: get navigation 2018-04-13 14:18:13,001 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:13,001 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/nav 2018-04-13 14:18:13,002 DEBUG quick_setup running python command "catnav" 2018-04-13 14:18:13,003 INFO quick_subs navigation file nav/a_rb.gps created from load/*.gps2 2018-04-13 14:18:13,004 INFO quick_subs navigation file nav/a_rb.agt created from load/*.gpst2 2018-04-13 14:18:13,006 DEBUG quick_mpl Starting plot: uvship 2018-04-13 14:18:13,742 DEBUG quick_mpl Ending plot: uvship 2018-04-13 14:18:13,742 INFO quick_run plotted uvship 2018-04-13 14:18:13,742 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:13,742 INFO quick_adcp step 8: list heading 2018-04-13 14:18:13,743 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2018-04-13 14:18:13,743 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:13,743 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/cal/rotate 2018-04-13 14:18:13,743 DEBUG quick_setup running python command "lst_hdg" 2018-04-13 14:18:13,743 DEBUG quick_subs dbname: ../../adcpdb/a_rb output: scn.hdg step_size= 1 year_base= 2018 time_ranges: all 2018-04-13 14:18:13,743 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2018-04-13 14:18:13,757 INFO quick_run ... headings extracted 2018-04-13 14:18:13,758 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:13,758 INFO quick_adcp step 9: plot heading correction 2018-04-13 14:18:13,758 DEBUG quick_run hcorr_inst is posmv 2018-04-13 14:18:13,758 DEBUG quick_mpl Starting plot: hcorr 2018-04-13 14:18:13,771 DEBUG quick_mpl found 2.350699 days of data 2018-04-13 14:18:13,771 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2018-04-13 14:18:13,772 DEBUG quick_mpl printing 1 pages 2018-04-13 14:18:14,514 DEBUG quick_mpl Ending plot: hcorr 2018-04-13 14:18:14,514 INFO quick_run plots are in cal/rotate/*png 2018-04-13 14:18:14,514 INFO quick_adcp ------------------------- 2018-04-13 14:18:14,514 INFO quick_adcp ---- running navsteps --- 2018-04-13 14:18:14,514 INFO quick_adcp ------------------------- 2018-04-13 14:18:14,514 INFO quick_adcp step 10: nav steps: run adcpsect 2018-04-13 14:18:14,514 INFO quick_adcp navstep 1 2018-04-13 14:18:14,514 DEBUG quick_setup nav/as_nav.tmp exists 2018-04-13 14:18:14,515 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:14,515 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/nav 2018-04-13 14:18:14,515 DEBUG quick_setup running python command "as_nav" 2018-04-13 14:18:14,515 DEBUG quick_subs dbname: ../adcpdb/a_rb output: a_rb 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 2018/04/11 05:52:51 to 2018/04/13 14:17:52 /* the whole time range */ 2018-04-13 14:18:14,515 DEBUG quick_setup about to run adcpsect as_nav.tmp 2018-04-13 14:18:14,545 INFO quick_run ... ran adcpsect for navsteps 2018-04-13 14:18:14,545 INFO quick_adcp ------------------------- 2018-04-13 14:18:14,545 INFO quick_adcp step 11: nav steps: run refabs 2018-04-13 14:18:14,545 INFO quick_adcp navstep 2 2018-04-13 14:18:14,546 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:14,546 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/nav 2018-04-13 14:18:14,546 DEBUG quick_setup running python command "refabs" 2018-04-13 14:18:14,546 DEBUG quick_subs fix_file_type: simple reference_file: a_rb.nav fix_file: a_rb.gps output: a_rb.ref year_base= 2018 ensemble_length= 300 gap_tolerance= 10 2018-04-13 14:18:14,546 DEBUG quick_setup about to run refabs refabs.tmp 2018-04-13 14:18:14,555 INFO quick_run ... ran refabs for navsteps 2018-04-13 14:18:14,555 INFO quick_adcp ------------------------- 2018-04-13 14:18:14,555 INFO quick_adcp step 12: nav steps: run smoothr for plots 2018-04-13 14:18:14,555 INFO quick_adcp navstep 3 2018-04-13 14:18:14,555 DEBUG quick_setup nav/smoothr.tmp exists 2018-04-13 14:18:14,555 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:14,555 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/nav 2018-04-13 14:18:14,556 DEBUG quick_setup running python command "smoothr" 2018-04-13 14:18:14,556 DEBUG quick_subs reference_file: a_rb.nav refabs_output: a_rb.ref output: a_rb.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 2018-04-13 14:18:14,556 DEBUG quick_setup about to run smoothr smoothr.tmp 2018-04-13 14:18:14,590 INFO quick_run ... ran smoothr 2018-04-13 14:18:14,591 INFO quick_adcp ------------------------- 2018-04-13 14:18:14,591 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2018-04-13 14:18:14,591 INFO quick_adcp navstep 4 2018-04-13 14:18:14,591 INFO quick_run smoothing method for ship speed: refsm 2018-04-13 14:18:14,591 INFO quick_run smoothing window: 3 2018-04-13 14:18:14,591 INFO quick_run ship speed source: nav 2018-04-13 14:18:14,591 DEBUG quick_npy Starting: refsm 2018-04-13 14:18:14,640 DEBUG quick_npy Ending: refsm 2018-04-13 14:18:14,641 INFO quick_run ... shipspeed smoothing step done 2018-04-13 14:18:14,641 INFO quick_adcp ------------------------- 2018-04-13 14:18:14,641 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2018-04-13 14:18:14,641 INFO quick_adcp navstep 5 2018-04-13 14:18:14,641 DEBUG quick_setup nav/put_txy.tmp exists 2018-04-13 14:18:14,641 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:14,641 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/nav 2018-04-13 14:18:14,641 DEBUG quick_setup running python command "put_txy" 2018-04-13 14:18:14,641 DEBUG quick_subs dbname: ../adcpdb/a_rb position_file: a_rb.agt year_base= 2018 tolerance= 5 2018-04-13 14:18:14,641 DEBUG quick_setup about to run put_txy put_txy.tmp 2018-04-13 14:18:14,652 INFO quick_run ... ran put_txy 2018-04-13 14:18:14,652 DEBUG quick_setup nav/put_tuv.tmp exists 2018-04-13 14:18:14,652 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:14,653 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/nav 2018-04-13 14:18:14,653 DEBUG quick_setup running python command "put_tuv" 2018-04-13 14:18:14,653 DEBUG quick_subs dbname: ../adcpdb/a_rb shipspeed_file: refsm_tuv.asc year_base= 2018 tolerance= 5 2018-04-13 14:18:14,653 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2018-04-13 14:18:14,662 INFO quick_run ... ran put_tuv 2018-04-13 14:18:14,663 DEBUG quick_mpl Starting plot: nav 2018-04-13 14:18:15,057 DEBUG quick_mpl Ending plot: nav 2018-04-13 14:18:15,057 INFO quick_run ... made navigation plot 2018-04-13 14:18:15,057 INFO quick_adcp ------------------------- 2018-04-13 14:18:15,057 INFO quick_adcp step 15: nav steps: make reflayer plots 2018-04-13 14:18:15,058 INFO quick_adcp navstep 6 2018-04-13 14:18:15,058 DEBUG quick_mpl Starting plot: refl 2018-04-13 14:18:15,092 DEBUG quick_mpl found 2.340247 days of data 2018-04-13 14:18:15,093 DEBUG quick_mpl start day is 100.000000 2018-04-13 14:18:15,093 DEBUG quick_mpl figures with 2.000000 days per page 2018-04-13 14:18:15,093 DEBUG quick_mpl printing 2 pages 2018-04-13 14:18:15,093 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2018-04-13 14:18:16,009 DEBUG quick_mpl Ending plot: refl 2018-04-13 14:18:16,009 INFO quick_run ... made reflayer plots 2018-04-13 14:18:16,010 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:16,010 INFO quick_adcp step 10: find profile flags 2018-04-13 14:18:16,010 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:16,010 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/edit 2018-04-13 14:18:16,010 DEBUG quick_setup running python command "run_autoedit_npy" 2018-04-13 14:18:16,010 DEBUG quick_npy Starting: autoedit 2018-04-13 14:18:16,060 DEBUG pingedit wrote 2 bad bins to abadbin_tmp.asc 2018-04-13 14:18:16,063 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2018-04-13 14:18:16,063 DEBUG quick_npy Ending: autoedit 2018-04-13 14:18:16,063 INFO quick_run ... extracted files using automatic editing 2018-04-13 14:18:16,063 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:16,063 INFO quick_adcp step 11: apply editing 2018-04-13 14:18:16,064 DEBUG quick_run starting in: /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:16,064 DEBUG quick_run executing commands from: edit 2018-04-13 14:18:16,065 DEBUG quick_run about to run dbupdate ../adcpdb/a_rb abadprf_tmp.asc 2018-04-13 14:18:16,070 DEBUG quick_run about to run badbin ../adcpdb/a_rb abadbin_tmp.asc 2018-04-13 14:18:16,074 DEBUG quick_subs dbname: ../adcpdb/a_rb pg_min: 50 set_range_bit time_ranges: all 2018-04-13 14:18:16,075 DEBUG quick_run about to run setflags setflags.tmp 2018-04-13 14:18:16,086 DEBUG quick_run changing directories back to /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:16,086 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:16,086 INFO quick_adcp step 12: run calibration steps 2018-04-13 14:18:16,086 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2018-04-13 14:18:16,086 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:16,086 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/cal/botmtrk 2018-04-13 14:18:16,087 DEBUG quick_setup running python command "lst_btrk" 2018-04-13 14:18:16,087 DEBUG quick_subs dbname: ../../adcpdb/a_rb output: a_rb.btm step_size= 1 year_base= 2018 time_ranges: 2018/04/11 05:52:51 to 2018/04/13 14:17:52 /* whole time range */ 2018-04-13 14:18:16,087 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2018-04-13 14:18:16,093 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2018-04-13 14:18:16,093 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:16,093 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/cal/botmtrk 2018-04-13 14:18:16,093 DEBUG quick_setup running python command "refabsbt" 2018-04-13 14:18:16,094 DEBUG quick_subs fix_file_type: simple reference_file: a_rb.btm fix_file: ../../nav/a_rb.gps output: a_rb.ref year_base= 2018 ensemble_length= 300 gap_tolerance= 60 2018-04-13 14:18:16,094 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2018-04-13 14:18:16,098 INFO quick_run ...bottom track info in check cal/botmtrk 2018-04-13 14:18:16,098 DEBUG quick_mpl Starting plot: btcal 2018-04-13 14:18:16,099 DEBUG quick_mpl No data in a_rb.btm 2018-04-13 14:18:16,099 DEBUG quick_mpl Returning from Btplot with no output 2018-04-13 14:18:16,099 DEBUG quick_mpl Ending plot: btcal 2018-04-13 14:18:16,099 DEBUG quick_setup nav/as_nav.tmp exists 2018-04-13 14:18:16,099 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:16,099 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/nav 2018-04-13 14:18:16,099 DEBUG quick_setup running python command "as_nav" 2018-04-13 14:18:16,100 DEBUG quick_subs dbname: ../adcpdb/a_rb output: a_rb 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 2018/04/11 05:52:51 to 2018/04/13 14:17:52 /* the whole time range */ 2018-04-13 14:18:16,100 DEBUG quick_setup about to run adcpsect as_nav.tmp 2018-04-13 14:18:16,113 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2018-04-13 14:18:16,114 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:16,114 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/cal/watertrk 2018-04-13 14:18:16,114 DEBUG quick_setup running python command "timslip" 2018-04-13 14:18:16,114 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_rb.gps reference_file: ../../nav/a_rb.nav output_file: a_rb_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 2018-04-13 14:18:16,114 DEBUG quick_setup about to run timslip timslip.tmp 2018-04-13 14:18:16,120 INFO quick_run ... watertrack info in cal/watertrk 2018-04-13 14:18:16,120 DEBUG quick_mpl Starting plot: wtcal 2018-04-13 14:18:16,121 DEBUG quick_mpl Found 2 calibration points 2018-04-13 14:18:17,300 DEBUG quick_mpl Ending plot: wtcal 2018-04-13 14:18:17,300 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:17,300 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/cal/watertrk 2018-04-13 14:18:17,300 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2018-04-13 14:18:17,300 DEBUG quick_npy Starting: guess_xducerxy 2018-04-13 14:18:17,338 DEBUG quick_npy Ending: guess_xducerxy 2018-04-13 14:18:17,339 INFO quick_run ... check cal/watertrk for estimate 2018-04-13 14:18:17,339 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:17,339 INFO quick_adcp step 13: extract and plot temperature 2018-04-13 14:18:17,339 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:17,339 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/edit 2018-04-13 14:18:17,339 DEBUG quick_setup running python command "lst_temp" 2018-04-13 14:18:17,339 DEBUG quick_subs dbname: ../adcpdb/a_rb output: a_rb.tem step_size= 1 year_base= 2018 time_ranges: all 2018-04-13 14:18:17,339 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2018-04-13 14:18:17,350 DEBUG quick_mpl Starting plot: temp 2018-04-13 14:18:17,357 DEBUG quick_mpl plotting 678 points 2018-04-13 14:18:17,654 DEBUG quick_mpl Ending plot: temp 2018-04-13 14:18:17,654 INFO quick_run plotted temperature 2018-04-13 14:18:17,654 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:17,654 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2018-04-13 14:18:17,654 DEBUG quick_setup edit/lst_npings.tmp exists 2018-04-13 14:18:17,655 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:17,655 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/edit 2018-04-13 14:18:17,655 DEBUG quick_setup running python command "lst_npings" 2018-04-13 14:18:17,655 DEBUG quick_subs dbname: ../adcpdb/a_rb output: a_rb_npings.txt step_size= 1 year_base= 2018 time_ranges: all 2018-04-13 14:18:17,655 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2018-04-13 14:18:17,665 DEBUG quick_mpl Starting plot: npings 2018-04-13 14:18:17,671 DEBUG quick_mpl plotting 678 points 2018-04-13 14:18:17,812 DEBUG quick_mpl Ending plot: npings 2018-04-13 14:18:17,812 INFO quick_run ... plotted number of pings per ensemble 2018-04-13 14:18:17,813 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:17,813 INFO quick_adcp step 15: extract matlab "allbins" 2018-04-13 14:18:17,813 DEBUG quick_asect step 18: make matlab files for plotting 2018-04-13 14:18:17,813 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:17,813 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/vector 2018-04-13 14:18:17,813 DEBUG quick_setup running python command "timegrid" 2018-04-13 14:18:17,813 DEBUG quick_setup about to run timegrid a_rb.tmp 2018-04-13 14:18:17,819 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:17,819 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/vector 2018-04-13 14:18:17,819 DEBUG quick_setup running python command "as_vect" 2018-04-13 14:18:17,819 DEBUG quick_setup about to run adcpsect as_vect.tmp 2018-04-13 14:18:17,838 DEBUG quick_asect done making vector matfiles 2018-04-13 14:18:17,838 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:17,838 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/contour 2018-04-13 14:18:17,838 DEBUG quick_setup running python command "timegrid" 2018-04-13 14:18:17,839 DEBUG quick_setup about to run timegrid a_rb.tmp 2018-04-13 14:18:17,844 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:17,844 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/contour 2018-04-13 14:18:17,844 DEBUG quick_setup running python command "as_cont" 2018-04-13 14:18:17,844 DEBUG quick_setup about to run adcpsect as_cont.tmp 2018-04-13 14:18:17,869 DEBUG quick_setup starting in /home/data/RB1802_2/proc/os75nb 2018-04-13 14:18:17,869 DEBUG quick_setup executing commands from /home/data/RB1802_2/proc/os75nb/contour 2018-04-13 14:18:17,869 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_rb 2018-04-13 14:18:17,914 DEBUG quick_asect done running getmat with "allbins" 2018-04-13 14:18:17,914 INFO quick_adcp --------------------------------------------- 2018-04-13 14:18:17,914 INFO quick_adcp writing "cruise_info.txt" 2018-04-13 14:18:17,916 INFO root copying NOFIG to /home/adcp/www/figures/os75nb_hcorr_plot.png 2018-04-13 14:18:17,916 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os75nb_hcorr_plot_thumb.png 2018-04-13 14:18:17,917 DEBUG root matfile is contour/contour_uv.mat 2018-04-13 14:18:17,917 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os75nb_cont_uv.mat 2018-04-13 14:18:17,917 DEBUG root matfile is vector/vector_uv.mat 2018-04-13 14:18:17,918 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os75nb_vect_uv.mat 2018-04-13 14:18:17,918 DEBUG root matfile is contour/contour_xy.mat 2018-04-13 14:18:17,918 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os75nb_cont_xy.mat 2018-04-13 14:18:17,918 DEBUG root matfile is vector/vector_xy.mat 2018-04-13 14:18:17,918 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os75nb_vect_xy.mat 2018-04-13 14:18:17,918 DEBUG root about to copy file edit/a_rb.tem to /home/adcp/www/data/os75nb_temp.asc 2018-04-13 14:18:17,919 INFO root copying edit/a_rb.tem to /home/adcp/www/data/os75nb_temp.asc 2018-04-13 14:18:17,921 ERROR root cannot make os75nb netcdf file Traceback (most recent call last): File "/usr/local/currents/bin/run_quick.py", line 244, in from pycurrents.adcp.adcp_nc import make_nc_short File "/usr/local/lib/python2.7/dist-packages/pycurrents/adcp/adcp_nc.py", line 38, in from netCDF4 import Dataset ImportError: No module named netCDF4 2018-04-13 14:18:17,943 ERROR root cannot make compressed os75nb netcdf file Traceback (most recent call last): File "/usr/local/currents/bin/run_quick.py", line 282, in from pycurrents.adcp.adcp_nc import make_nc_compressed File "/usr/local/lib/python2.7/dist-packages/pycurrents/adcp/adcp_nc.py", line 38, in from netCDF4 import Dataset ImportError: No module named netCDF4 2018-04-13 14:18:17,972 INFO root generating pingstats for os75nb 2018-04-13 14:18:17,972 INFO root Ending quick_adcp.py