2012-06-17 11:19:45,002 DEBUG root about to write control file parameters to --yearbase 2012 --cruisename at21_02 --configtype python --sonar wh300 --dbname a_at --datatype uhdas --cfgpath /home/data/at21_02/proc/wh300/config --ens_len 120 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea --skip_avg ## see above --max_search_depth 500 --proc_engine python --incremental --find_pflags --hidedisplay --top_plotbin 1 --auto 2012-06-17 11:19:45,008 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d wh300 2012-06-17 11:19:45,011 DEBUG quick_adcp progdir = /home/currents/programs 2012-06-17 11:19:45,012 DEBUG quick_adcp binos = lnx 2012-06-17 11:19:45,018 DEBUG quick_setup found cruise_info.hcorr (phins, hdg, 0) 2012-06-17 11:19:45,025 INFO quick_adcp importing numpy 2012-06-17 11:19:45,114 INFO quick_adcp importing matplotlib 2012-06-17 11:19:45,306 DEBUG quick_mpl in Q_mpl 2012-06-17 11:19:45,306 DEBUG quick_adcp ------processor dictionary:------ __doc__ __init__ __module__ aflagit_setup as_cont as_nav as_vect asetup catnav check_beamangle check_dbinfo check_headcorr check_opts check_uhdascfg clearflags ddtime def_qlist del_overlapping fill_thisload_timerange get_asvars get_cmd_timerange get_nodb_times get_time_range getmat ldcodas listblocks llgrid loadping lst_btrk lst_conf lst_hdg lst_temp mpltest norotate opts plotbtcal_mpl plothcorr_mpl plotnav_mpl plotrefl_mpl plottemp_mpl plotwtcal_mpl putnav refabs refabsbt rotate rotated run_adcpsect run_applyedit run_autoedit_npy run_calc run_calib run_editsetup run_findpflags run_getheadcorr run_getnav run_guess_xducerxy run_guess_xducerxy_npy run_loaddb run_loadlta_npy run_loadping run_lstconfig run_lsthdg run_lsttemp run_matbincmd run_matfiles run_pingavg_npy run_plotter run_putnav run_py_codaseditsetup run_py_findpflags run_py_pingeditsetup run_pybincmd_lta run_pybincmd_uhdas run_pygbin_npy run_refabs run_refplots run_refsm run_refsm_npy run_rotate run_scanbin_npy run_scandata run_scanlta_npy run_scanping_npy run_setflags run_smoothr run_updategbin run_updatepygbin run_xducerxy run_xducerxy_npy scanping setflags smoothr timegrid timslip ubprint write_codas_editdefaults write_ping_editdefaults write_timerange_file zapsetup 2012-06-17 11:19:45,306 INFO quick_adcp cwd is /home/data/at21_02/proc/wh300 about to run these steps: - editsetup - scandata - avg_and_load - setflags - getnav - get_headcorr - rotate - adcpsect - refabs - smoothnav - putnav - refplots - find_pflags - apply_edit - navsteps - lst_temp - calib - matfiles - find_pflags 2012-06-17 11:19:45,307 INFO quick_adcp original fix file is a_at.gps 2012-06-17 11:19:45,307 INFO quick_adcp smoothed nav file is a_at_refsm.asc 2012-06-17 11:19:45,307 DEBUG quick_asect extracting matlab files for wh300, bb pings 2012-06-17 11:19:45,421 DEBUG quick_setup data directory: /home/data/at21_02/raw/wh300 2012-06-17 11:19:45,425 INFO quick_setup found 193 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/at21_02/raw/wh300/*.raw" 2012-06-17 11:19:45,427 DEBUG quick_setup found 193 files from original filelist 2012-06-17 11:19:45,427 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/at21_02/raw/wh300/at2012_151_62215.raw ... 2012-06-17 11:19:45,430 DEBUG quick_adcp Sun Jun 17 11:19:45 2012 running quick_adcp.py as follows: --cntfile /home/data/at21_02/proc/wh300/wh300_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_at dbpath ../adcpdb deeper_boundaries [40, 60, 80, 100, 120] firstdepth 9 gridnum 80 increment 2 loaded_time_range all numbins 128 outdir . pgmin 50 prefix allbins_ proc_yearbase 2012 rl_endbin 20 rl_startbin 2 ss_string separate timegrid 60 vbasename vector ----- quick_adcp.py variables and current values ------ adjust_time 1 auto True badbeam None beamangle 20 best_loggerdday_name unix_dday best_utcdday_name dday bindir /home/currents/programs/codas3/bin/lnx binos lnx btrk_step 1 cfgpath /home/data/at21_02/proc/wh300/config cntfile /home/data/at21_02/proc/wh300/wh300_qpy.cnt commands None configtype python cruisename at21_02 data_def vmadcp.def datadir /home/data/at21_02/raw/wh300 datafile_glob *.raw datatype uhdas dbname a_at dday_bailout None debug False diarystr %% no diary written %% displaystr set(0,'defaultfigureposition',[0 0 300 400]) set(0,'defaultfiguremenubar','none') set(0,'defaultfiguretoolbar','none') ducer_depth None editcfg_file override_editcfg enddday_file None ens_halign None ens_len 300 ensgyrorbin False expert None filelist ['/home/data/at21_02/raw/wh300/at2012_151_62215.raw', '/home/data/at21_02/raw/wh300/at2012_152_50748.raw', '/home/data/at21_02/raw/wh300/at2012_152_57600.raw', '/home/data/at21_02/raw/wh300/at2012_152_58778.raw', '/home/data/at21_02/raw/wh300/at2012_152_64800.raw', '/home/data/at21_02/raw/wh300/at2012_152_72000.raw', '/home/data/at21_02/raw/wh300/at2012_152_79200.raw', '/home/data/at21_02/raw/wh300/at2012_153_00000.raw', 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'/home/data/at21_02/raw/wh300/at2012_168_07200.raw', '/home/data/at21_02/raw/wh300/at2012_168_14400.raw', '/home/data/at21_02/raw/wh300/at2012_168_21600.raw', '/home/data/at21_02/raw/wh300/at2012_168_28800.raw', '/home/data/at21_02/raw/wh300/at2012_168_36000.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 9 fixfile a_at.gps frequency 300 gbin_style python gbindirbase /home/data/at21_02/gbin hcorr_inst phins help False hidedisplay True incremental True instname wh300 jitter 15 max_BLKprofiles 300 max_search_depth 500 maxrunsecs None min_filter_fraction 0.5 model wh nosave_editcfg 0 num_persistence 24 numbins 128 overview False pgmin 50 ping_headcorr False pingtype bb post_headcorr None printformats png proc_engine python proc_yearbase 2012 progdir /home/currents/programs py_gbindirbase /home/data/at21_02/gbin rawstd_cutoff None rl_endbin 20 rl_startbin 2 rotate_amplitude 1 rotate_angle 0 rotate_file None save_editcfg 1 save_lastens 0 setup_info False skip_avg True smfile a_at_refsm.asc sonar wh300 steps2rerun timeout_secs 86400 tips False tktail False top_plotbin 1 ub_type 1920 update_gbin False use_refsm True use_smoothr False vardoc False varvals False wtrk_step 7 xducer_dx None xducer_dy None yearbase 2012 configured to run the following steps: editsetup scandata avg_and_load setflags getnav get_headcorr rotate adcpsect refabs smoothnav putnav refplots find_pflags apply_edit navsteps lst_temp calib matfiles find_pflags 2012-06-17 11:19:45,431 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:45,431 INFO quick_adcp step 1: set up editing files 2012-06-17 11:19:45,431 DEBUG quick_run executing commands from /home/data/at21_02/proc/wh300/edit 2012-06-17 11:19:45,432 DEBUG quick_run setup.m exists. not replacing 2012-06-17 11:19:45,432 DEBUG quick_run asetup.m exists. not replacing 2012-06-17 11:19:45,432 DEBUG quick_run aflagit_setup.m exists. not replacing 2012-06-17 11:19:45,432 DEBUG quick_subs dbname: ../adcpdb/a_at pg_min: 50 clear_range /* reset range */ clear_all_bits /* clear flags except pg_min*/ clear_bad_profile /* reset access vars lgb */ time_ranges: all 2012-06-17 11:19:45,433 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:45,433 INFO quick_adcp step 2: scan files for time range 2012-06-17 11:19:45,433 INFO quick_adcp about to run numpy scan, requiring python gbins 2012-06-17 11:19:45,434 DEBUG quick_npy Starting: scanping 2012-06-17 11:19:47,942 DEBUG quick_npy Ending: scanping 2012-06-17 11:19:47,945 DEBUG quick_subs start_end_time 2012/05/31 17:16:56 to 2012/06/01 14:20:02 2012-06-17 11:19:47,945 DEBUG quick_subs dd0: 151.720093 dd1: 152.597245 2012-06-17 11:19:47,945 INFO quick_adcp in quick_adcp.py: after scan; look for database times in /home/data/at21_02/proc/wh300 2012-06-17 11:19:47,946 INFO quick_adcp looking for database with adcpdb/a_at*.blk 2012-06-17 11:19:47,947 INFO quick_adcp database found: listing blocks 2012-06-17 11:19:47,948 DEBUG quick_subs removing a_atdir.blk 2012-06-17 11:19:47,948 DEBUG quick_subs about to run mkblkdir 2012-06-17 11:19:47,949 DEBUG quick_subs database still exists; rerunning mkdirblk 2012-06-17 11:19:47,949 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2012-06-17 11:19:48,002 DEBUG quick_subs database passes. 2012-06-17 11:19:48,003 DEBUG quick_subs start_end_time 2012/06/01 14:07:49 to 2012/06/17 11:04:06 2012-06-17 11:19:48,003 DEBUG quick_subs dd0: 152.588762 dd1: 168.461181 2012-06-17 11:19:48,004 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2012-06-17 11:19:48,004 DEBUG quick_adcp origdb_time_range is 2012/06/01 14:07:49 to 2012/06/17 11:04:06 2012-06-17 11:19:48,005 DEBUG quick_adcp (152.588762 to 168.461181) 2012-06-17 11:19:48,005 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:48,005 INFO quick_adcp step 3: generate averaged data... 2012-06-17 11:19:48,005 DEBUG quick_run file load/ping_editparams.txt exists. not replacing 2012-06-17 11:19:48,006 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:19:48,006 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/load 2012-06-17 11:19:48,006 DEBUG quick_setup running python command "run_pingavg_npy" 2012-06-17 11:19:48,006 DEBUG quick_npy Starting: pingavg 2012-06-17 11:19:48,011 DEBUG quick_npy singleping editing parameters: 2012-06-17 11:19:48,011 DEBUG quick_npy bigtarget_mab_window : 11 2012-06-17 11:19:48,011 DEBUG quick_npy rl_endbin : 20 2012-06-17 11:19:48,012 DEBUG quick_npy max_search_depth : 500 2012-06-17 11:19:48,012 DEBUG quick_npy cor_cutoff : 70 2012-06-17 11:19:48,012 DEBUG quick_npy ampfilt : 40 2012-06-17 11:19:48,012 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2012-06-17 11:19:48,012 DEBUG quick_npy rl_startbin : 2 2012-06-17 11:19:48,013 DEBUG quick_npy ecutoff : 1 2012-06-17 11:19:48,013 DEBUG quick_npy refavg_valcutoff : 1 2012-06-17 11:19:48,013 DEBUG quick_npy weakprof_percent : 30 2012-06-17 11:19:48,013 DEBUG quick_npy bigtarget_ampthresh : 55 2012-06-17 11:19:48,025 INFO pingavg Pingavg.run for time range 168.416669 to 168.471059 2012-06-17 11:19:48,124 DEBUG pingavg Chunk 1 of 1, 168.416669 to 168.471059 2012-06-17 11:19:48,125 DEBUG pingavg Nothing written 2012-06-17 11:19:48,125 DEBUG quick_npy wrote 0 averages 2012-06-17 11:19:48,126 DEBUG quick_npy Ending: pingavg 2012-06-17 11:19:48,127 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:48,127 INFO quick_adcp step 4: load averaged data (to database) 2012-06-17 11:19:48,129 DEBUG quick_subs in del_overlapping 2012-06-17 11:19:48,130 DEBUG quick_subs lastblock: 2012-06-17 11:19:48,130 DEBUG quick_subs 39 2012-06-17 11:19:48,130 DEBUG quick_subs lastcmd: 2012-06-17 11:19:48,130 DEBUG quick_subs 39 2012-06-17 11:19:48,130 DEBUG quick_subs delblks: 2012-06-17 11:19:48,131 DEBUG quick_subs [39] 2012-06-17 11:19:48,131 DEBUG quick_subs loadblks: 2012-06-17 11:19:48,131 DEBUG quick_subs [39] 2012-06-17 11:19:48,132 DEBUG quick_subs about to run mkblkdir 2012-06-17 11:19:48,133 DEBUG quick_subs database still exists; rerunning mkdirblk 2012-06-17 11:19:48,133 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2012-06-17 11:19:48,151 DEBUG quick_subs database passes. 2012-06-17 11:19:48,154 DEBUG quick_subs start_end_time 2012/06/01 14:07:49 to 2012/06/17 08:08:05 2012-06-17 11:19:48,154 DEBUG quick_subs dd0: 152.588762 dd1: 168.338947 2012-06-17 11:19:48,155 DEBUG quick_run [39] 2012-06-17 11:19:48,155 DEBUG quick_run cmdlist 2012-06-17 11:19:48,155 DEBUG quick_run ['./ens_blk039.cmd'] 2012-06-17 11:19:48,159 INFO quick_run Warning: 1 files will be loaded; 39 already exist 2012-06-17 11:19:48,159 INFO quick_run Sun Jun 17 11:19:48 2012 2012-06-17 11:19:48,159 INFO quick_run about to load uhdas files 2012-06-17 11:19:48,159 INFO quick_run /home/data/at21_02/raw/wh300/at2012_151_62215.raw /home/data/at21_02/raw/wh300/at2012_152_50748.raw /home/data/at21_02/raw/wh300/at2012_152_57600.raw /home/data/at21_02/raw/wh300/at2012_152_58778.raw /home/data/at21_02/raw/wh300/at2012_152_64800.raw ... 2012-06-17 11:19:48,160 DEBUG quick_setup load/ldcodas.tmp exists 2012-06-17 11:19:48,160 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:19:48,160 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/load 2012-06-17 11:19:48,161 DEBUG quick_setup running python command "ldcodas" 2012-06-17 11:19:48,161 DEBUG quick_subs filling "thisload" timerange 2012-06-17 11:19:48,163 DEBUG quick_subs in ldcodas 2012-06-17 11:19:48,163 DEBUG quick_subs cmdlist: 2012-06-17 11:19:48,163 DEBUG quick_subs ['./ens_blk039.cmd'] 2012-06-17 11:19:48,164 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_at DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2012 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk039.cmd 2012-06-17 11:19:48,164 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/ldcodas ldcodas.tmp 2012-06-17 11:19:48,218 DEBUG quick_subs removing a_atdir.blk 2012-06-17 11:19:48,219 DEBUG quick_subs about to run mkblkdir 2012-06-17 11:19:48,219 DEBUG quick_subs database still exists; rerunning mkdirblk 2012-06-17 11:19:48,219 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2012-06-17 11:19:48,238 DEBUG quick_subs database passes. 2012-06-17 11:19:48,239 DEBUG quick_subs start_end_time 2012/06/01 14:07:49 to 2012/06/17 11:18:05 2012-06-17 11:19:48,239 DEBUG quick_subs dd0: 152.588762 dd1: 168.470891 2012-06-17 11:19:48,240 INFO quick_adcp loaded_time_range is 2012/06/01 14:07:49 to 2012/06/17 11:18:05 2012-06-17 11:19:48,241 INFO quick_adcp (152.588762 to 168.470891) 2012-06-17 11:19:48,241 INFO quick_adcp origdb_time_range is 2012/06/01 14:07:49 to 2012/06/17 11:04:06 2012-06-17 11:19:48,241 INFO quick_adcp (152.588762 to 168.461181) 2012-06-17 11:19:48,241 INFO quick_adcp thisload_time_range is 2012/06/17 08:10:06 to 2012/06/17 11:18:05 2012-06-17 11:19:48,242 INFO quick_adcp (168.340347 to 168.340347) 2012-06-17 11:19:48,242 INFO quick_adcp --------------------- 2012-06-17 11:19:48,242 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:19:48,243 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/adcpdb 2012-06-17 11:19:48,243 DEBUG quick_setup running python command "lst_conf" 2012-06-17 11:19:48,243 DEBUG quick_subs dbname: a_at output: a_at.cnh time_ranges: all 2012-06-17 11:19:48,243 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_conf lst_conf.tmp 2012-06-17 11:19:51,002 DEBUG quick_setup found (in edit/asetup.m): 2012-06-17 11:19:51,003 DEBUG quick_setup config.beamangle is 20 2012-06-17 11:19:51,003 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:51,003 INFO quick_adcp step 5: set up files for gautoedit.py 2012-06-17 11:19:51,004 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2012-06-17 11:19:51,004 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:51,009 INFO quick_adcp step 6: set up files for gautoedit.py 2012-06-17 11:19:51,009 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:19:51,009 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/edit 2012-06-17 11:19:51,010 DEBUG quick_setup running python command "setflags" 2012-06-17 11:19:51,010 DEBUG quick_subs dbname: ../adcpdb/a_at pg_min: 50 set_range_bit time_ranges: all 2012-06-17 11:19:51,010 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/setflags setflags.tmp 2012-06-17 11:19:51,271 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:51,272 INFO quick_adcp step 7: get navigation 2012-06-17 11:19:51,272 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:19:51,273 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/nav 2012-06-17 11:19:51,273 DEBUG quick_setup running python command "catnav" 2012-06-17 11:19:51,284 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2012-06-17 11:19:51,284 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:19:51,285 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/cal/rotate 2012-06-17 11:19:51,285 DEBUG quick_setup running python command "lst_hdg" 2012-06-17 11:19:51,285 DEBUG quick_subs dbname: ../../adcpdb/a_at output: scn.hdg step_size= 1 year_base= 2012 time_ranges: all 2012-06-17 11:19:51,286 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_hdg lst_hdg.tmp 2012-06-17 11:19:51,485 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:51,486 INFO quick_adcp step 8: get heading correction 2012-06-17 11:19:51,486 DEBUG quick_run hcorr_inst is phins 2012-06-17 11:19:51,486 DEBUG quick_mpl Starting plot: hcorr 2012-06-17 11:19:51,866 DEBUG quick_mplplots found 15.882136 days of data 2012-06-17 11:19:51,867 DEBUG quick_mplplots figures with 4 panels per page, 1.000000 days per panel 2012-06-17 11:19:51,867 DEBUG quick_mplplots printing 5 pages 2012-06-17 11:19:53,818 DEBUG quick_mpl Ending plot: hcorr 2012-06-17 11:19:53,819 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:53,819 INFO quick_adcp step 9: rotate velocities 2012-06-17 11:19:53,820 DEBUG quick_setup cal/rotate/norotate.tmp exists 2012-06-17 11:19:53,824 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:19:53,824 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/cal/rotate 2012-06-17 11:19:53,825 DEBUG quick_setup running python command "norotate" 2012-06-17 11:19:53,825 DEBUG quick_subs /* No rotation was done using the "rotate" command, but */ /* it is useful have the skeleton of a rotate.tmp file */ /* to edit, should the need arise. That is the purpose */ /* of this file. */ DB_NAME: ../../adcpdb/a_at LOG_FILE: rotate.log TIME_RANGE: 2012/06/01 14:07:49 to 2012/06/17 11:18:05 OPTION_LIST: water_and_bottom_track: year_base= 2012 /* time_angle_file: time_angle.ang */ amplitude= 1.0 angle_0= 0.0 end end 2012-06-17 11:19:53,825 DEBUG quick_setup about to run echo "writing dummy rotate file" 2012-06-17 11:19:53,840 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:53,841 INFO quick_adcp step 10: nav steps: run adcpsect 2012-06-17 11:19:53,841 DEBUG quick_setup nav/as_nav.tmp exists 2012-06-17 11:19:53,841 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:19:53,841 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/nav 2012-06-17 11:19:53,842 DEBUG quick_setup running python command "as_nav" 2012-06-17 11:19:53,842 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at step_size: 1 ndepth: 20 time_ranges: separate year_base= 2012 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 2012/06/01 14:07:49 to 2012/06/17 11:18:05 /* the whole time range */ 2012-06-17 11:19:53,842 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2012-06-17 11:19:54,272 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:54,273 INFO quick_adcp step 11: nav steps: run refabs 2012-06-17 11:19:54,274 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:19:54,274 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/nav 2012-06-17 11:19:54,274 DEBUG quick_setup running python command "refabs" 2012-06-17 11:19:54,275 DEBUG quick_subs fix_file_type: simple reference_file: a_at.nav fix_file: a_at.gps output: a_at.ref year_base= 2012 ensemble_length= 300 gap_tolerance= 10 2012-06-17 11:19:54,275 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabs refabs.tmp 2012-06-17 11:19:54,624 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:54,625 INFO quick_adcp step 12: nav steps: run smoothr for plots 2012-06-17 11:19:54,625 DEBUG quick_setup nav/smoothr.tmp exists 2012-06-17 11:19:54,625 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:19:54,626 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/nav 2012-06-17 11:19:54,626 DEBUG quick_setup running python command "smoothr" 2012-06-17 11:19:54,626 DEBUG quick_subs reference_file: a_at.nav refabs_output: a_at.ref output: a_at.sm filter_hwidth= 0.0208 min_filter_fraction= 0.5 max_gap_ratio= 0.05 max_gap_distance= 50 max_gap_time= 30 /* 0.5 minutes */ ensemble_time= 300 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2012-06-17 11:19:54,627 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/smoothr smoothr.tmp 2012-06-17 11:19:56,169 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:56,170 INFO quick_adcp step 13: nav steps: smooth navigation 2012-06-17 11:19:56,170 INFO quick_adcp about to run numpy refsm 2012-06-17 11:19:56,171 DEBUG quick_npy Starting: refsm 2012-06-17 11:19:57,408 DEBUG nav dtmin = -0.50 dtmax = 1.63 2012-06-17 11:19:59,140 DEBUG quick_npy Ending: refsm 2012-06-17 11:19:59,141 INFO quick_adcp --------------------------------------------- 2012-06-17 11:19:59,141 INFO quick_adcp step 14: nav steps: put smoothed nav into codasdb 2012-06-17 11:19:59,141 DEBUG quick_setup nav/putnav.tmp exists 2012-06-17 11:19:59,142 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:19:59,142 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/nav 2012-06-17 11:19:59,142 DEBUG quick_setup running python command "putnav" 2012-06-17 11:19:59,142 DEBUG quick_subs dbname: ../adcpdb/a_at position_file: a_at_refsm.asc year_base= 2012 tolerance= 5 navigation_sources: gps end 2012-06-17 11:19:59,143 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/putnav putnav.tmp 2012-06-17 11:19:59,611 INFO quick_adcp plotting navigation 2012-06-17 11:19:59,611 DEBUG quick_mpl Starting plot: nav 2012-06-17 11:20:01,025 DEBUG quick_mpl Ending plot: nav 2012-06-17 11:20:01,026 INFO quick_adcp --------------------------------------------- 2012-06-17 11:20:01,026 INFO quick_adcp step 15: nav steps: make reflayer plots 2012-06-17 11:20:01,026 DEBUG quick_mpl Starting plot: refl 2012-06-17 11:20:01,926 DEBUG quick_mplplots found 15.879355 days of data 2012-06-17 11:20:01,926 DEBUG quick_mplplots start day is 152.000000 2012-06-17 11:20:01,927 DEBUG quick_mplplots figures with 2.000000 days per page 2012-06-17 11:20:01,927 DEBUG quick_mplplots printing 9 pages 2012-06-17 11:20:01,927 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2012-06-17 11:20:04,226 DEBUG quick_mpl Ending plot: refl 2012-06-17 11:20:04,226 INFO quick_adcp --------------------------------------------- 2012-06-17 11:20:04,227 INFO quick_adcp step 16: find profile flags 2012-06-17 11:20:04,227 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:04,227 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/edit 2012-06-17 11:20:04,228 DEBUG quick_setup running python command "run_autoedit_npy" 2012-06-17 11:20:04,228 DEBUG quick_npy Starting: autoedit 2012-06-17 11:20:06,398 DEBUG pingedit wrote 54 bad bins to abadbin_tmp.asc 2012-06-17 11:20:06,516 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2012-06-17 11:20:06,516 DEBUG quick_npy Ending: autoedit 2012-06-17 11:20:06,517 INFO quick_adcp --------------------------------------------- 2012-06-17 11:20:06,518 INFO quick_adcp step 17: apply editing 2012-06-17 11:20:06,519 DEBUG quick_run starting in: /home/data/at21_02/proc/wh300 2012-06-17 11:20:06,519 DEBUG quick_run executing commands from: edit 2012-06-17 11:20:06,524 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/dbupdate ../adcpdb/a_at abadprf_tmp.asc 2012-06-17 11:20:06,548 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/badbin ../adcpdb/a_at abadbin_tmp.asc 2012-06-17 11:20:06,578 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/set_lgb ../adcpdb/a_at 20 2012-06-17 11:20:06,596 DEBUG quick_subs dbname: ../adcpdb/a_at pg_min: 50 set_range_bit time_ranges: all 2012-06-17 11:20:06,597 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/setflags setflags.tmp 2012-06-17 11:20:06,930 DEBUG quick_run changing directories back to /home/data/at21_02/proc/wh300 2012-06-17 11:20:06,930 INFO quick_adcp --------------------------------------------- 2012-06-17 11:20:06,930 INFO quick_adcp step 18: run nav steps 2012-06-17 11:20:06,931 DEBUG quick_setup nav/as_nav.tmp exists 2012-06-17 11:20:06,931 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:06,931 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/nav 2012-06-17 11:20:06,932 DEBUG quick_setup running python command "as_nav" 2012-06-17 11:20:06,932 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at step_size: 1 ndepth: 20 time_ranges: separate year_base= 2012 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 2012/06/01 14:07:49 to 2012/06/17 11:18:05 /* the whole time range */ 2012-06-17 11:20:06,933 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2012-06-17 11:20:07,440 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:07,441 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/nav 2012-06-17 11:20:07,441 DEBUG quick_setup running python command "refabs" 2012-06-17 11:20:07,441 DEBUG quick_subs fix_file_type: simple reference_file: a_at.nav fix_file: a_at.gps output: a_at.ref year_base= 2012 ensemble_length= 300 gap_tolerance= 10 2012-06-17 11:20:07,442 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabs refabs.tmp 2012-06-17 11:20:07,778 DEBUG quick_setup nav/smoothr.tmp exists 2012-06-17 11:20:07,778 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:07,778 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/nav 2012-06-17 11:20:07,779 DEBUG quick_setup running python command "smoothr" 2012-06-17 11:20:07,779 DEBUG quick_subs reference_file: a_at.nav refabs_output: a_at.ref output: a_at.sm filter_hwidth= 0.0208 min_filter_fraction= 0.5 max_gap_ratio= 0.05 max_gap_distance= 50 max_gap_time= 30 /* 0.5 minutes */ ensemble_time= 300 max_speed= 5.0 min_speed= 1.0 iterations= 5 fix_to_dr_limit= 0.00050 2012-06-17 11:20:07,780 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/smoothr smoothr.tmp 2012-06-17 11:20:10,313 DEBUG quick_npy Starting: refsm 2012-06-17 11:20:11,974 DEBUG nav dtmin = -0.50 dtmax = 1.63 2012-06-17 11:20:13,636 DEBUG quick_npy Ending: refsm 2012-06-17 11:20:13,637 DEBUG quick_setup nav/putnav.tmp exists 2012-06-17 11:20:13,638 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:13,638 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/nav 2012-06-17 11:20:13,639 DEBUG quick_setup running python command "putnav" 2012-06-17 11:20:13,639 DEBUG quick_subs dbname: ../adcpdb/a_at position_file: a_at_refsm.asc year_base= 2012 tolerance= 5 navigation_sources: gps end 2012-06-17 11:20:13,641 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/putnav putnav.tmp 2012-06-17 11:20:14,276 DEBUG quick_mpl Starting plot: nav 2012-06-17 11:20:15,852 DEBUG quick_mpl Ending plot: nav 2012-06-17 11:20:15,853 DEBUG quick_mpl Starting plot: refl 2012-06-17 11:20:16,707 DEBUG quick_mplplots found 15.879355 days of data 2012-06-17 11:20:16,708 DEBUG quick_mplplots start day is 152.000000 2012-06-17 11:20:16,708 DEBUG quick_mplplots figures with 2.000000 days per page 2012-06-17 11:20:16,708 DEBUG quick_mplplots printing 9 pages 2012-06-17 11:20:16,708 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2012-06-17 11:20:18,452 DEBUG quick_mpl Ending plot: refl 2012-06-17 11:20:18,453 INFO quick_adcp --------------------------------------------- 2012-06-17 11:20:18,453 INFO quick_adcp step 19: plot temperature 2012-06-17 11:20:18,454 DEBUG quick_setup edit/lst_temp.tmp exists 2012-06-17 11:20:18,454 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:18,454 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/edit 2012-06-17 11:20:18,455 DEBUG quick_setup running python command "lst_temp" 2012-06-17 11:20:18,455 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at.tem step_size= 1 year_base= 2012 time_ranges: all 2012-06-17 11:20:18,456 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_temp lst_temp.tmp 2012-06-17 11:20:18,688 DEBUG quick_mpl Starting plot: temp 2012-06-17 11:20:19,106 DEBUG quick_mplplots plotting 11435 points 2012-06-17 11:20:20,119 DEBUG quick_mpl Ending plot: temp 2012-06-17 11:20:20,120 INFO quick_adcp --------------------------------------------- 2012-06-17 11:20:20,120 INFO quick_adcp step 20: run calibration steps 2012-06-17 11:20:20,121 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2012-06-17 11:20:20,121 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:20,121 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/cal/botmtrk 2012-06-17 11:20:20,121 DEBUG quick_setup running python command "lst_btrk" 2012-06-17 11:20:20,122 DEBUG quick_subs dbname: ../../adcpdb/a_at output: a_at.btm step_size= 1 year_base= 2012 time_ranges: 2012/06/01 14:07:49 to 2012/06/17 11:18:05 /* whole time range */ 2012-06-17 11:20:20,122 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_btrk lst_btrk.tmp 2012-06-17 11:20:20,256 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2012-06-17 11:20:20,256 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:20,256 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/cal/botmtrk 2012-06-17 11:20:20,257 DEBUG quick_setup running python command "refabsbt" 2012-06-17 11:20:20,257 DEBUG quick_subs fix_file_type: simple reference_file: a_at.btm fix_file: ../../nav/a_at.gps output: a_at.ref year_base= 2012 ensemble_length= 300 gap_tolerance= 60 2012-06-17 11:20:20,257 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabsbt refabsbt.tmp 2012-06-17 11:20:20,268 DEBUG quick_mpl Starting plot: btcal 2012-06-17 11:20:20,271 ERROR quick_mpl Failure in plot: btcal Traceback (most recent call last): File "/home/currents/programs/pycurrents/adcp/quick_mpl.py", line 40, in run_plotter Plotter() File "/home/currents/programs/pycurrents/adcp/quick_mplplots.py", line 847, in __call__ if not self.get_data(): File "/home/currents/programs/pycurrents/adcp/quick_mplplots.py", line 881, in get_data refi = rangeslice(refdat[:,0], self.ddrange) IndexError: invalid index 2012-06-17 11:20:20,273 DEBUG quick_mpl Ending plot: btcal 2012-06-17 11:20:20,273 DEBUG quick_setup nav/as_nav.tmp exists 2012-06-17 11:20:20,274 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:20,274 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/nav 2012-06-17 11:20:20,274 DEBUG quick_setup running python command "as_nav" 2012-06-17 11:20:20,274 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at step_size: 1 ndepth: 20 time_ranges: separate year_base= 2012 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 2012/06/01 14:07:49 to 2012/06/17 11:18:05 /* the whole time range */ 2012-06-17 11:20:20,275 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2012-06-17 11:20:20,697 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2012-06-17 11:20:20,697 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:20,698 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/cal/watertrk 2012-06-17 11:20:20,698 DEBUG quick_setup running python command "timslip" 2012-06-17 11:20:20,698 DEBUG quick_subs fix_file_type: simple fix_file: ../../nav/a_at.gps reference_file: ../../nav/a_at.nav output_file: a_at_7.cal year_base= 2012 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 2012-06-17 11:20:20,699 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timslip timslip.tmp 2012-06-17 11:20:20,893 DEBUG quick_mpl Starting plot: wtcal 2012-06-17 11:20:20,905 DEBUG quick_mplplots Found 86 calibration points 2012-06-17 11:20:23,022 DEBUG quick_mpl Ending plot: wtcal 2012-06-17 11:20:23,023 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:23,023 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/cal/watertrk 2012-06-17 11:20:23,023 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2012-06-17 11:20:23,024 DEBUG quick_npy Starting: guess_xducerxy 2012-06-17 11:20:24,686 DEBUG quick_npy Ending: guess_xducerxy 2012-06-17 11:20:24,686 INFO quick_adcp --------------------------------------------- 2012-06-17 11:20:24,686 INFO quick_adcp step 21: extract matlab "allbins" 2012-06-17 11:20:24,687 DEBUG quick_asect ------------ step 18: make matlab files for plotting ------------- 2012-06-17 11:20:24,687 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:24,687 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/vector 2012-06-17 11:20:24,687 DEBUG quick_setup running python command "timegrid" 2012-06-17 11:20:24,688 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timegrid a_at.tmp 2012-06-17 11:20:24,703 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:24,703 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/vector 2012-06-17 11:20:24,703 DEBUG quick_setup running python command "as_vect" 2012-06-17 11:20:24,704 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_vect.tmp 2012-06-17 11:20:25,121 DEBUG quick_asect done making vector matfiles 2012-06-17 11:20:25,122 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:25,122 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/contour 2012-06-17 11:20:25,122 DEBUG quick_setup running python command "timegrid" 2012-06-17 11:20:25,123 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timegrid a_at.tmp 2012-06-17 11:20:25,157 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:25,157 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/contour 2012-06-17 11:20:25,157 DEBUG quick_setup running python command "as_cont" 2012-06-17 11:20:25,158 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_cont.tmp 2012-06-17 11:20:25,997 DEBUG quick_setup starting in /home/data/at21_02/proc/wh300 2012-06-17 11:20:25,998 DEBUG quick_setup executing commands from /home/data/at21_02/proc/wh300/contour 2012-06-17 11:20:25,998 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_at 2012-06-17 11:20:27,943 DEBUG quick_asect done running getmat with "allbins" 2012-06-17 11:20:27,943 INFO quick_adcp --------------------------------------------- 2012-06-17 11:20:27,944 INFO quick_adcp step 22: write "cruise_info.txt" 2012-06-17 11:20:28,002 INFO root copying NOFIG to /home/adcp/www/figures/wh300_hcorr_plot.png 2012-06-17 11:20:28,002 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/wh300_hcorr_plot_thumb.png 2012-06-17 11:20:28,003 DEBUG root matfile is contour/contour_uv.mat 2012-06-17 11:20:28,013 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/wh300_cont_uv.mat 2012-06-17 11:20:28,013 DEBUG root matfile is vector/vector_uv.mat 2012-06-17 11:20:28,015 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/wh300_vect_uv.mat 2012-06-17 11:20:28,015 DEBUG root matfile is contour/contour_xy.mat 2012-06-17 11:20:28,016 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/wh300_cont_xy.mat 2012-06-17 11:20:28,016 DEBUG root matfile is vector/vector_xy.mat 2012-06-17 11:20:28,017 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/wh300_vect_xy.mat 2012-06-17 11:20:28,017 DEBUG root about to copy file edit/a_at.tem to /home/adcp/www/data/wh300_temp.asc 2012-06-17 11:20:28,034 INFO root copying edit/a_at.tem to /home/adcp/www/data/wh300_temp.asc 2012-06-17 11:20:33,241 DEBUG root about to copy netcdf file /home/data/at21_02/proc/wh300/contour/wh300.nc to /home/adcp/www/data/wh300.nc 2012-06-17 11:20:33,299 INFO root copying edit/a_at.tem to /home/adcp/www/data/wh300.nc 2012-06-17 11:20:33,542 INFO root generating pingstats for wh300 2012-06-17 11:20:33,542 INFO root Ending quick_adcp.py