2016-11-07 21:09:16,235 DEBUG root about to write control file parameters to --yearbase 2016 --cruisename SR1611 --configtype python --sonar os38nb --dbname a_sr --datatype uhdas --cfgpath /home/data/SR1611/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 0 --xducer_dy 0 ## see config/SR1611_proc.py for other settings --skip_avg ## see above --max_search_depth 2000 --ping_headcorr --proc_engine python --refuv_smoothwin 3 --incremental --find_pflags --top_plotbin 1 --auto 2016-11-07 21:09:16,236 DEBUG quick_adcp sys.argv = /usr/local/currents/bin/run_quick.py -d os38nb 2016-11-07 21:09:16,238 DEBUG quick_setup found cruise_info.hcorr (seapath, sea, 0) 2016-11-07 21:09:16,238 DEBUG quick_setup no heading correction will be used within the ensembles but values are staged in cal/rotate/hcorr.asc 2016-11-07 21:09:16,238 INFO quick_setup fix file is a_sr.gps 2016-11-07 21:09:16,238 INFO quick_setup reflayer: ref_method = refsm 2016-11-07 21:09:16,238 INFO quick_setup reflayer: refuv_source = nav 2016-11-07 21:09:16,238 INFO quick_setup reflayer: refuv_smoothwin = 3 2016-11-07 21:09:16,239 INFO quick_adcp importing numpy version 1.8.2 2016-11-07 21:09:16,252 INFO quick_adcp importing matplotlib version 1.4.3 2016-11-07 21:09:16,412 DEBUG quick_mpl in Q_mpl 2016-11-07 21:09:16,412 INFO quick_adcp ===================================================== 2016-11-07 21:09:16,412 INFO quick_adcp ===================================================== 2016-11-07 21:09:16,412 INFO quick_adcp command line was: /usr/local/currents/bin/run_quick.py -d os38nb 2016-11-07 21:09:16,412 INFO quick_adcp cwd is /home/data/SR1611/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 2016-11-07 21:09:16,412 DEBUG quick_asect extracting matlab files for os38nb 2016-11-07 21:09:16,415 DEBUG quick_setup data directory: /home/data/SR1611/raw/os38 2016-11-07 21:09:16,415 INFO quick_setup found 15 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/SR1611/raw/os38/*.raw" 2016-11-07 21:09:16,415 DEBUG quick_setup found 15 files from original filelist 2016-11-07 21:09:16,415 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/SR1611/raw/os38/sr2016_310_59930.raw ... 2016-11-07 21:09:16,416 DEBUG quick_adcp Mon Nov 7 21:09:16 2016 running quick_adcp.py as follows: --cntfile /home/data/SR1611/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 2016 rl_endbin 20 rl_startbin 2 ss_string separate timegrid 60 vbasename vector ----- quick_adcp.py variables and current values ------ adjust_time 1 auto True badbeam None beamangle 30 bl_half_width 3 btrk_step 1.5 cfgpath /home/data/SR1611/proc/os38nb/config cntfile /home/data/SR1611/proc/os38nb/os38nb_qpy.cnt commands None configtype python cruisename SR1611 data_def vmadcp.def datadir /home/data/SR1611/raw/os38 datafile_glob *.raw datatype uhdas dbname a_sr dday_bailout None debug False ens_len 300 expert None filelist ['/home/data/SR1611/raw/os38/sr2016_310_59930.raw', '/home/data/SR1611/raw/os38/sr2016_310_64800.raw', '/home/data/SR1611/raw/os38/sr2016_310_72000.raw', '/home/data/SR1611/raw/os38/sr2016_310_79200.raw', '/home/data/SR1611/raw/os38/sr2016_311_00000.raw', '/home/data/SR1611/raw/os38/sr2016_311_07200.raw', '/home/data/SR1611/raw/os38/sr2016_311_14400.raw', '/home/data/SR1611/raw/os38/sr2016_311_21600.raw', '/home/data/SR1611/raw/os38/sr2016_311_28800.raw', '/home/data/SR1611/raw/os38/sr2016_311_36000.raw', '/home/data/SR1611/raw/os38/sr2016_311_43200.raw', '/home/data/SR1611/raw/os38/sr2016_311_50400.raw', '/home/data/SR1611/raw/os38/sr2016_311_57600.raw', '/home/data/SR1611/raw/os38/sr2016_311_64800.raw', '/home/data/SR1611/raw/os38/sr2016_311_72000.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 2016 py_gbindirbase /home/data/SR1611/gbin ref_method refsm refuv_inputfile a_sr.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 os38nb 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_sr.gps ub_type 1920 uhdas_config yearbase = 2016 uhdas_dir = /home/data/SR1611 sonar = os38nb gbin = /home/data/SR1611/gbin gbinsonar = /home/data/SR1611/gbin/os38 raw = /home/data/SR1611/raw rawsonar = /home/data/SR1611/raw/os38 rbin = /home/data/SR1611/rbin proc = /home/data/SR1611/proc procsonar = /home/data/SR1611/proc/os38nb other attributes: gbin_params = hdg_inst : gyro hdg_inst_msgs : [('gyro', 'hdg'), ('seapath', 'sea'), ('hydrins', 'hdg')] hdg_msg : hdg pitch_inst : seapath pitch_msg : sea pos_inst : seapath pos_msg : gps roll_inst : seapath roll_msg : sea hcorr = ['seapath', 'sea', 0.0] acc_heading_cutoff = 0.02 update_gbin False vardoc False varvals False wtrk_step 7 xducer_dx 0 xducer_dy 0 yearbase 2016 configured to run the following steps: write_clearflags scandata avg_and_load codaseditsetup setflags getnav lst_hdg plot_headcorr navsteps find_pflags apply_edit navsteps lst_temp plot_temp lst_npings calib matfiles adcpsect refabs smoothnav putnav refplots find_pflags codaseditsetup 2016-11-07 21:09:16,416 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:16,416 INFO quick_adcp step 1: set up files in "edit" directory 2016-11-07 21:09:16,416 INFO quick_run file exists (edit/clearflags.tmp). not writing 2016-11-07 21:09:16,416 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:16,416 INFO quick_adcp step 2: scan files for time range 2016-11-07 21:09:16,416 DEBUG quick_npy Starting: scanping 2016-11-07 21:09:16,432 DEBUG quick_npy Ending: scanping 2016-11-07 21:09:16,432 DEBUG quick_subs start_end_time 2016/11/06 16:38:53 to 2016/11/06 16:49:05 2016-11-07 21:09:16,432 DEBUG quick_subs dd0: 310.693669 dd1: 310.700752 2016-11-07 21:09:16,433 INFO quick_adcp looking for database with adcpdb/a_sr*.blk 2016-11-07 21:09:16,433 INFO quick_adcp database found: listing blocks 2016-11-07 21:09:16,433 DEBUG quick_subs removing a_srdir.blk 2016-11-07 21:09:16,433 DEBUG quick_subs about to run mkblkdir 2016-11-07 21:09:16,433 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-11-07 21:09:16,433 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-11-07 21:09:16,441 DEBUG quick_subs database passes. 2016-11-07 21:09:16,442 DEBUG quick_subs start_end_time 2016/11/06 16:43:50 to 2016/11/07 20:53:53 2016-11-07 21:09:16,442 DEBUG quick_subs dd0: 310.697106 dd1: 311.870752 2016-11-07 21:09:16,442 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2016-11-07 21:09:16,442 DEBUG quick_adcp origdb_time_range is 2016/11/06 16:43:50 to 2016/11/07 20:53:53 2016-11-07 21:09:16,442 DEBUG quick_adcp (310.697106 to 311.870752) 2016-11-07 21:09:16,442 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:16,442 INFO quick_adcp step 3: generate averaged data... 2016-11-07 21:09:16,442 INFO quick_run file load/ping_editparams.txt exists. not replacing 2016-11-07 21:09:16,443 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:16,443 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/load 2016-11-07 21:09:16,443 DEBUG quick_setup running python command "run_pingavg_npy" 2016-11-07 21:09:16,443 DEBUG quick_npy Starting: pingavg 2016-11-07 21:09:16,444 DEBUG quick_npy xducerxy is [0, 0] 2016-11-07 21:09:16,445 DEBUG quick_npy singleping editing parameters: 2016-11-07 21:09:16,445 DEBUG quick_npy bigtarget_mab_window : 11 2016-11-07 21:09:16,445 DEBUG quick_npy rl_endbin : 20 2016-11-07 21:09:16,445 DEBUG quick_npy max_search_depth : 2000 2016-11-07 21:09:16,445 DEBUG quick_npy cor_cutoff : 120 2016-11-07 21:09:16,445 DEBUG quick_npy ampfilt : 40 2016-11-07 21:09:16,445 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2016-11-07 21:09:16,445 DEBUG quick_npy rl_startbin : 2 2016-11-07 21:09:16,445 DEBUG quick_npy ecutoff : 0.800000 2016-11-07 21:09:16,445 DEBUG quick_npy refavg_valcutoff : 1 2016-11-07 21:09:16,445 DEBUG quick_npy weakprof_percent : 30 2016-11-07 21:09:16,445 DEBUG quick_npy bigtarget_ampthresh : 55 2016-11-07 21:09:16,449 INFO pingavg ---------------- 2016-11-07 21:09:16,449 INFO pingavg sonar is os38nb 2016-11-07 21:09:16,449 INFO pingavg Pingavg.run for time range 311.833355 to 311.881374 2016-11-07 21:09:16,449 INFO pingavg transducer offset: xducer_dx = 0.000, xducer_dy = 0.000 2016-11-07 21:09:16,449 INFO pingavg shifted positions applied to *.gpst2 and *.uvship' 2016-11-07 21:09:16,449 INFO pingavg ---------------- 2016-11-07 21:09:16,465 DEBUG pingavg Chunk 1 of 1, 311.833355 to 311.881374 2016-11-07 21:09:16,465 DEBUG pingavg Nothing written 2016-11-07 21:09:16,465 DEBUG quick_npy wrote 0 averages 2016-11-07 21:09:16,466 DEBUG quick_npy Ending: pingavg 2016-11-07 21:09:16,466 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:16,467 INFO quick_adcp step 4: load averaged data (to database) 2016-11-07 21:09:16,467 DEBUG quick_subs in del_overlapping 2016-11-07 21:09:16,467 DEBUG quick_subs lastblock: 2016-11-07 21:09:16,467 DEBUG quick_subs 2 2016-11-07 21:09:16,467 DEBUG quick_subs lastcmd: 2016-11-07 21:09:16,467 DEBUG quick_subs 2 2016-11-07 21:09:16,467 DEBUG quick_subs delblks: 2016-11-07 21:09:16,467 DEBUG quick_subs [2] 2016-11-07 21:09:16,467 DEBUG quick_subs loadblks: 2016-11-07 21:09:16,467 DEBUG quick_subs [2] 2016-11-07 21:09:16,468 DEBUG quick_subs about to run mkblkdir 2016-11-07 21:09:16,468 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-11-07 21:09:16,468 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-11-07 21:09:16,476 DEBUG quick_subs database passes. 2016-11-07 21:09:16,476 DEBUG quick_subs start_end_time 2016/11/06 16:43:50 to 2016/11/07 17:38:53 2016-11-07 21:09:16,476 DEBUG quick_subs dd0: 310.697106 dd1: 311.735336 2016-11-07 21:09:16,477 DEBUG quick_run [2] 2016-11-07 21:09:16,477 DEBUG quick_run cmdlist 2016-11-07 21:09:16,477 DEBUG quick_run ['./ens_blk002.cmd'] 2016-11-07 21:09:16,478 INFO quick_run loaded time range: 2016/11/07 17:43:53 to 2016/11/07 21:08:53 2016-11-07 21:09:16,478 DEBUG quick_setup load/ldcodas.tmp exists 2016-11-07 21:09:16,478 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:16,478 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/load 2016-11-07 21:09:16,479 DEBUG quick_setup running python command "ldcodas" 2016-11-07 21:09:16,479 DEBUG quick_subs filling "thisload" timerange 2016-11-07 21:09:16,479 DEBUG quick_subs in ldcodas 2016-11-07 21:09:16,479 DEBUG quick_subs cmdlist: 2016-11-07 21:09:16,480 DEBUG quick_subs ['./ens_blk002.cmd'] 2016-11-07 21:09:16,480 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_sr DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2016 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk002.cmd 2016-11-07 21:09:16,480 DEBUG quick_setup about to run ldcodas ldcodas.tmp 2016-11-07 21:09:16,492 INFO quick_run 3 block files present 2016-11-07 21:09:16,493 DEBUG quick_subs removing a_srdir.blk 2016-11-07 21:09:16,493 DEBUG quick_subs about to run mkblkdir 2016-11-07 21:09:16,493 DEBUG quick_subs database still exists; rerunning mkdirblk 2016-11-07 21:09:16,493 DEBUG quick_subs running mkblkdir mkblkdir.tmp 2016-11-07 21:09:16,500 DEBUG quick_subs database passes. 2016-11-07 21:09:16,500 DEBUG quick_subs start_end_time 2016/11/06 16:43:50 to 2016/11/07 21:08:53 2016-11-07 21:09:16,500 DEBUG quick_subs dd0: 310.697106 dd1: 311.881169 2016-11-07 21:09:16,501 INFO quick_adcp database time range: 2016-11-07 21:09:16,501 INFO quick_adcp 2016/11/06 16:43:50 to 2016/11/07 21:08:53 2016-11-07 21:09:16,501 INFO quick_adcp (310.697106 to 311.881169) 2016-11-07 21:09:16,501 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:16,501 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/adcpdb 2016-11-07 21:09:16,501 DEBUG quick_setup running python command "lst_conf" 2016-11-07 21:09:16,501 DEBUG quick_subs dbname: a_sr output: a_sr.cnh time_ranges: all 2016-11-07 21:09:16,501 DEBUG quick_setup about to run lst_conf lst_conf.tmp 2016-11-07 21:09:16,509 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:16,509 INFO quick_adcp step 5: set up files for codas editing (gautoedit.py) 2016-11-07 21:09:16,510 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2016-11-07 21:09:16,510 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:16,510 INFO quick_adcp step 6: run setflags? 2016-11-07 21:09:16,510 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:16,510 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/edit 2016-11-07 21:09:16,510 DEBUG quick_setup running python command "write_setflags" 2016-11-07 21:09:16,510 DEBUG quick_subs dbname: ../adcpdb/a_sr pg_min: 50 set_range_bit time_ranges: all 2016-11-07 21:09:16,510 DEBUG quick_setup about to run setflags setflags.tmp 2016-11-07 21:09:16,522 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:16,522 INFO quick_adcp step 7: get navigation 2016-11-07 21:09:16,522 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:16,523 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/nav 2016-11-07 21:09:16,523 DEBUG quick_setup running python command "catnav" 2016-11-07 21:09:16,524 INFO quick_subs navigation file nav/a_sr.gps created from load/*.gps2 2016-11-07 21:09:16,525 INFO quick_subs navigation file nav/a_sr.agt created from load/*.gpst2 2016-11-07 21:09:16,525 DEBUG quick_mpl Starting plot: uvship 2016-11-07 21:09:16,853 DEBUG quick_mpl Ending plot: uvship 2016-11-07 21:09:16,853 INFO quick_run plotted uvship 2016-11-07 21:09:16,853 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:16,853 INFO quick_adcp step 8: list heading 2016-11-07 21:09:16,854 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2016-11-07 21:09:16,854 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:16,854 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/cal/rotate 2016-11-07 21:09:16,854 DEBUG quick_setup running python command "lst_hdg" 2016-11-07 21:09:16,854 DEBUG quick_subs dbname: ../../adcpdb/a_sr output: scn.hdg step_size= 1 year_base= 2016 time_ranges: all 2016-11-07 21:09:16,854 DEBUG quick_setup about to run lst_hdg lst_hdg.tmp 2016-11-07 21:09:16,860 INFO quick_run ... headings extracted 2016-11-07 21:09:16,861 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:16,861 INFO quick_adcp step 9: plot heading correction 2016-11-07 21:09:16,861 DEBUG quick_run hcorr_inst is seapath 2016-11-07 21:09:16,861 DEBUG quick_mpl Starting plot: hcorr 2016-11-07 21:09:16,864 DEBUG quick_mpl found 1.184054 days of data 2016-11-07 21:09:16,864 DEBUG quick_mpl figures with 4 panels per page, 1.000000 days per panel 2016-11-07 21:09:16,864 DEBUG quick_mpl printing 1 pages 2016-11-07 21:09:17,159 DEBUG quick_mpl Ending plot: hcorr 2016-11-07 21:09:17,159 INFO quick_run plots are in cal/rotate/*png 2016-11-07 21:09:17,159 INFO quick_adcp ------------------------- 2016-11-07 21:09:17,159 INFO quick_adcp ---- running navsteps --- 2016-11-07 21:09:17,159 INFO quick_adcp ------------------------- 2016-11-07 21:09:17,159 INFO quick_adcp step 10: nav steps: run adcpsect 2016-11-07 21:09:17,159 INFO quick_adcp navstep 1 2016-11-07 21:09:17,159 DEBUG quick_setup nav/as_nav.tmp exists 2016-11-07 21:09:17,159 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,159 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/nav 2016-11-07 21:09:17,159 DEBUG quick_setup running python command "as_nav" 2016-11-07 21:09:17,159 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2016 option_list: pg_min= 50 navigation: reference_bins 2 to 20 end statistics: mean units= 0.01 /* cm/s instead of default m/s */ end flag_mask: ALL_BITS end end 2016/11/06 16:43:50 to 2016/11/07 21:08:53 /* the whole time range */ 2016-11-07 21:09:17,160 DEBUG quick_setup about to run adcpsect as_nav.tmp 2016-11-07 21:09:17,169 INFO quick_run ... ran adcpsect for navsteps 2016-11-07 21:09:17,169 INFO quick_adcp ------------------------- 2016-11-07 21:09:17,169 INFO quick_adcp step 11: nav steps: run refabs 2016-11-07 21:09:17,170 INFO quick_adcp navstep 2 2016-11-07 21:09:17,170 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,170 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/nav 2016-11-07 21:09:17,170 DEBUG quick_setup running python command "refabs" 2016-11-07 21:09:17,170 DEBUG quick_subs fix_file_type: simple reference_file: a_sr.nav fix_file: a_sr.gps output: a_sr.ref year_base= 2016 ensemble_length= 300 gap_tolerance= 10 2016-11-07 21:09:17,170 DEBUG quick_setup about to run refabs refabs.tmp 2016-11-07 21:09:17,183 INFO quick_run ... ran refabs for navsteps 2016-11-07 21:09:17,184 INFO quick_adcp ------------------------- 2016-11-07 21:09:17,184 INFO quick_adcp step 12: nav steps: run smoothr for plots 2016-11-07 21:09:17,184 INFO quick_adcp navstep 3 2016-11-07 21:09:17,184 DEBUG quick_setup nav/smoothr.tmp exists 2016-11-07 21:09:17,184 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,184 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/nav 2016-11-07 21:09:17,184 DEBUG quick_setup running python command "smoothr" 2016-11-07 21:09:17,184 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 2016-11-07 21:09:17,185 DEBUG quick_setup about to run smoothr smoothr.tmp 2016-11-07 21:09:17,203 INFO quick_run ... ran smoothr 2016-11-07 21:09:17,204 INFO quick_adcp ------------------------- 2016-11-07 21:09:17,204 INFO quick_adcp step 13: nav steps: smooth navigation for velocities 2016-11-07 21:09:17,204 INFO quick_adcp navstep 4 2016-11-07 21:09:17,204 INFO quick_run smoothing method for ship speed: refsm 2016-11-07 21:09:17,204 INFO quick_run smoothing window: 3 2016-11-07 21:09:17,204 INFO quick_run ship speed source: nav 2016-11-07 21:09:17,204 DEBUG quick_npy Starting: refsm 2016-11-07 21:09:17,232 DEBUG quick_npy Ending: refsm 2016-11-07 21:09:17,232 INFO quick_run ... shipspeed smoothing step done 2016-11-07 21:09:17,232 INFO quick_adcp ------------------------- 2016-11-07 21:09:17,232 INFO quick_adcp step 14: nav steps: put positions and uvship from refsm into codasdb 2016-11-07 21:09:17,233 INFO quick_adcp navstep 5 2016-11-07 21:09:17,233 DEBUG quick_setup nav/put_txy.tmp exists 2016-11-07 21:09:17,233 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,233 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/nav 2016-11-07 21:09:17,233 DEBUG quick_setup running python command "put_txy" 2016-11-07 21:09:17,233 DEBUG quick_subs dbname: ../adcpdb/a_sr position_file: a_sr.gps year_base= 2016 tolerance= 5 2016-11-07 21:09:17,233 DEBUG quick_setup about to run put_txy put_txy.tmp 2016-11-07 21:09:17,241 INFO quick_run ... ran put_txy 2016-11-07 21:09:17,241 DEBUG quick_setup nav/put_tuv.tmp exists 2016-11-07 21:09:17,241 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,241 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/nav 2016-11-07 21:09:17,241 DEBUG quick_setup running python command "put_tuv" 2016-11-07 21:09:17,242 DEBUG quick_subs dbname: ../adcpdb/a_sr shipspeed_file: refsm_tuv.asc year_base= 2016 tolerance= 5 2016-11-07 21:09:17,242 DEBUG quick_setup about to run put_tuv put_tuv.tmp 2016-11-07 21:09:17,250 INFO quick_run ... ran put_tuv 2016-11-07 21:09:17,250 DEBUG quick_mpl Starting plot: nav 2016-11-07 21:09:17,522 DEBUG quick_mpl Ending plot: nav 2016-11-07 21:09:17,522 INFO quick_run ... made navigation plot 2016-11-07 21:09:17,522 INFO quick_adcp ------------------------- 2016-11-07 21:09:17,522 INFO quick_adcp step 15: nav steps: make reflayer plots 2016-11-07 21:09:17,522 INFO quick_adcp navstep 6 2016-11-07 21:09:17,523 DEBUG quick_mpl Starting plot: refl 2016-11-07 21:09:17,530 DEBUG quick_mpl found 1.173603 days of data 2016-11-07 21:09:17,531 DEBUG quick_mpl start day is 310.000000 2016-11-07 21:09:17,531 DEBUG quick_mpl figures with 2.000000 days per page 2016-11-07 21:09:17,531 DEBUG quick_mpl printing 1 pages 2016-11-07 21:09:17,531 DEBUG quick_mpl yrange will be [1.000000, 1.000000] 2016-11-07 21:09:17,826 DEBUG quick_mpl Ending plot: refl 2016-11-07 21:09:17,826 INFO quick_run ... made reflayer plots 2016-11-07 21:09:17,826 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:17,826 INFO quick_adcp step 10: find profile flags 2016-11-07 21:09:17,826 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,826 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/edit 2016-11-07 21:09:17,826 DEBUG quick_setup running python command "run_autoedit_npy" 2016-11-07 21:09:17,826 DEBUG quick_npy Starting: autoedit 2016-11-07 21:09:17,860 DEBUG pingedit wrote 8 bad bins to abadbin_tmp.asc 2016-11-07 21:09:17,863 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2016-11-07 21:09:17,863 DEBUG quick_npy Ending: autoedit 2016-11-07 21:09:17,863 INFO quick_run ... extracted files using automatic editing 2016-11-07 21:09:17,863 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:17,863 INFO quick_adcp step 11: apply editing 2016-11-07 21:09:17,863 DEBUG quick_run starting in: /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,863 DEBUG quick_run executing commands from: edit 2016-11-07 21:09:17,864 DEBUG quick_run about to run dbupdate ../adcpdb/a_sr abadprf_tmp.asc 2016-11-07 21:09:17,869 DEBUG quick_run about to run badbin ../adcpdb/a_sr abadbin_tmp.asc 2016-11-07 21:09:17,875 DEBUG quick_subs dbname: ../adcpdb/a_sr pg_min: 50 set_range_bit time_ranges: all 2016-11-07 21:09:17,875 DEBUG quick_run about to run setflags setflags.tmp 2016-11-07 21:09:17,887 DEBUG quick_run changing directories back to /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,887 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:17,887 INFO quick_adcp step 12: run calibration steps 2016-11-07 21:09:17,888 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2016-11-07 21:09:17,888 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,888 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/cal/botmtrk 2016-11-07 21:09:17,888 DEBUG quick_setup running python command "lst_btrk" 2016-11-07 21:09:17,888 DEBUG quick_subs dbname: ../../adcpdb/a_sr output: a_sr.btm step_size= 1 year_base= 2016 time_ranges: 2016/11/06 16:43:50 to 2016/11/07 21:08:53 /* whole time range */ 2016-11-07 21:09:17,888 DEBUG quick_setup about to run lst_btrk lst_btrk.tmp 2016-11-07 21:09:17,898 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2016-11-07 21:09:17,898 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,898 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/cal/botmtrk 2016-11-07 21:09:17,898 DEBUG quick_setup running python command "refabsbt" 2016-11-07 21:09:17,898 DEBUG quick_subs fix_file_type: simple reference_file: a_sr.btm fix_file: ../../nav/a_sr.gps output: a_sr.ref year_base= 2016 ensemble_length= 300 gap_tolerance= 60 2016-11-07 21:09:17,899 DEBUG quick_setup about to run refabsbt refabsbt.tmp 2016-11-07 21:09:17,906 INFO quick_run ...bottom track info in check cal/botmtrk 2016-11-07 21:09:17,907 DEBUG quick_mpl Starting plot: btcal 2016-11-07 21:09:17,908 DEBUG quick_mpl No data in a_sr.btm 2016-11-07 21:09:17,908 DEBUG quick_mpl Returning from Btplot with no output 2016-11-07 21:09:17,908 DEBUG quick_mpl Ending plot: btcal 2016-11-07 21:09:17,908 DEBUG quick_setup nav/as_nav.tmp exists 2016-11-07 21:09:17,908 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,908 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/nav 2016-11-07 21:09:17,908 DEBUG quick_setup running python command "as_nav" 2016-11-07 21:09:17,908 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr step_size: 1 ndepth: 20 time_ranges: separate year_base= 2016 option_list: pg_min= 50 navigation: reference_bins 2 to 20 end statistics: mean units= 0.01 /* cm/s instead of default m/s */ end flag_mask: ALL_BITS end end 2016/11/06 16:43:50 to 2016/11/07 21:08:53 /* the whole time range */ 2016-11-07 21:09:17,909 DEBUG quick_setup about to run adcpsect as_nav.tmp 2016-11-07 21:09:17,925 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2016-11-07 21:09:17,925 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,925 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/cal/watertrk 2016-11-07 21:09:17,925 DEBUG quick_setup running python command "timslip" 2016-11-07 21:09:17,926 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_sr.gps reference_file: ../../nav/a_sr.nav output_file: a_sr_7.cal year_base= 2016 min_n_fixes= 7 /* 5 7 9 */ n_refs= 7 /* 5 7 9 */ i_ref_l0= 1 i_ref_l1= 2 /* 1 2 3 */ i_ref_r0= 5 /* 4 5 6 */ i_ref_r1= 6 /* 4 6 8 */ up_thresh= 3.0 /* m/s */ down_thresh= 3.0 /* m/s */ turn_speed= 2.0 /* m/s */ turn_thresh= 60 /* degrees */ dtmax= 360 /* seconds, for 300-second ensembles */ tolerance= 5.e-5 /* days, about 5 seconds */ grid: ensemble use_shifted_times? no 2016-11-07 21:09:17,926 DEBUG quick_setup about to run timslip timslip.tmp 2016-11-07 21:09:17,936 INFO quick_run ... watertrack info in cal/watertrk 2016-11-07 21:09:17,936 DEBUG quick_mpl Starting plot: wtcal 2016-11-07 21:09:17,938 DEBUG quick_mpl Found 13 calibration points 2016-11-07 21:09:17,939 DEBUG quick_mpl Only 0 valid points found; quitting 2016-11-07 21:09:17,939 DEBUG quick_mpl Ending plot: wtcal 2016-11-07 21:09:17,939 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,939 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/cal/watertrk 2016-11-07 21:09:17,939 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2016-11-07 21:09:17,939 DEBUG quick_npy Starting: guess_xducerxy 2016-11-07 21:09:17,967 DEBUG quick_npy Ending: guess_xducerxy 2016-11-07 21:09:17,968 INFO quick_run ... check cal/watertrk for estimate 2016-11-07 21:09:17,968 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:17,968 INFO quick_adcp step 13: extract and plot temperature 2016-11-07 21:09:17,968 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:17,968 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/edit 2016-11-07 21:09:17,968 DEBUG quick_setup running python command "lst_temp" 2016-11-07 21:09:17,968 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr.tem step_size= 1 year_base= 2016 time_ranges: all 2016-11-07 21:09:17,968 DEBUG quick_setup about to run lst_temp lst_temp.tmp 2016-11-07 21:09:17,976 DEBUG quick_mpl Starting plot: temp 2016-11-07 21:09:17,979 DEBUG quick_mpl plotting 342 points 2016-11-07 21:09:18,232 DEBUG quick_mpl Ending plot: temp 2016-11-07 21:09:18,232 INFO quick_run plotted temperature 2016-11-07 21:09:18,232 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:18,232 INFO quick_adcp step 14: extract and plot number of pings per ensemble 2016-11-07 21:09:18,233 DEBUG quick_setup edit/lst_npings.tmp exists 2016-11-07 21:09:18,233 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:18,233 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/edit 2016-11-07 21:09:18,233 DEBUG quick_setup running python command "lst_npings" 2016-11-07 21:09:18,233 DEBUG quick_subs dbname: ../adcpdb/a_sr output: a_sr_npings.txt step_size= 1 year_base= 2016 time_ranges: all 2016-11-07 21:09:18,233 DEBUG quick_setup about to run lst_npings lst_npings.tmp 2016-11-07 21:09:18,241 DEBUG quick_mpl Starting plot: npings 2016-11-07 21:09:18,244 DEBUG quick_mpl plotting 342 points 2016-11-07 21:09:18,367 DEBUG quick_mpl Ending plot: npings 2016-11-07 21:09:18,367 INFO quick_run ... plotted number of pings per ensemble 2016-11-07 21:09:18,367 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:18,367 INFO quick_adcp step 15: extract matlab "allbins" 2016-11-07 21:09:18,367 DEBUG quick_asect step 18: make matlab files for plotting 2016-11-07 21:09:18,367 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:18,367 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/vector 2016-11-07 21:09:18,367 DEBUG quick_setup running python command "timegrid" 2016-11-07 21:09:18,368 DEBUG quick_setup about to run timegrid a_sr.tmp 2016-11-07 21:09:18,373 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:18,373 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/vector 2016-11-07 21:09:18,373 DEBUG quick_setup running python command "as_vect" 2016-11-07 21:09:18,373 DEBUG quick_setup about to run adcpsect as_vect.tmp 2016-11-07 21:09:18,385 DEBUG quick_asect done making vector matfiles 2016-11-07 21:09:18,386 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:18,386 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/contour 2016-11-07 21:09:18,386 DEBUG quick_setup running python command "timegrid" 2016-11-07 21:09:18,386 DEBUG quick_setup about to run timegrid a_sr.tmp 2016-11-07 21:09:18,391 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:18,392 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/contour 2016-11-07 21:09:18,392 DEBUG quick_setup running python command "as_cont" 2016-11-07 21:09:18,392 DEBUG quick_setup about to run adcpsect as_cont.tmp 2016-11-07 21:09:18,410 DEBUG quick_setup starting in /home/data/SR1611/proc/os38nb 2016-11-07 21:09:18,410 DEBUG quick_setup executing commands from /home/data/SR1611/proc/os38nb/contour 2016-11-07 21:09:18,411 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_sr 2016-11-07 21:09:18,435 DEBUG quick_asect done running getmat with "allbins" 2016-11-07 21:09:18,436 INFO quick_adcp --------------------------------------------- 2016-11-07 21:09:18,436 INFO quick_adcp writing "cruise_info.txt" 2016-11-07 21:09:18,437 INFO root copying NOFIG to /home/adcp/www/figures/os38nb_hcorr_plot.png 2016-11-07 21:09:18,437 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os38nb_hcorr_plot_thumb.png 2016-11-07 21:09:18,437 DEBUG root matfile is contour/contour_uv.mat 2016-11-07 21:09:18,438 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os38nb_cont_uv.mat 2016-11-07 21:09:18,438 DEBUG root matfile is vector/vector_uv.mat 2016-11-07 21:09:18,438 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os38nb_vect_uv.mat 2016-11-07 21:09:18,438 DEBUG root matfile is contour/contour_xy.mat 2016-11-07 21:09:18,438 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os38nb_cont_xy.mat 2016-11-07 21:09:18,438 DEBUG root matfile is vector/vector_xy.mat 2016-11-07 21:09:18,438 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os38nb_vect_xy.mat 2016-11-07 21:09:18,438 DEBUG root about to copy file edit/a_sr.tem to /home/adcp/www/data/os38nb_temp.asc 2016-11-07 21:09:18,439 INFO root copying edit/a_sr.tem to /home/adcp/www/data/os38nb_temp.asc 2016-11-07 21:09:18,509 DEBUG root about to copy netcdf file /home/data/SR1611/proc/os38nb/contour/os38nb.nc to /home/adcp/www/data/os38nb.nc 2016-11-07 21:09:18,509 INFO root copying edit/a_sr.tem to /home/adcp/www/data/os38nb.nc 2016-11-07 21:09:18,564 INFO root made compressed nc file /home/adcp/uhdas_tmp/os38nb_compr.nc in /home/adcp/uhdas_tmp 2016-11-07 21:09:18,573 INFO root generating pingstats for os38nb 2016-11-07 21:09:18,573 INFO root Ending quick_adcp.py