2014-08-06 14:13:49,671 DEBUG root about to write control file parameters to --yearbase 2014 --cruisename AT26_17 --configtype python --sonar os75nb --dbname a_at --datatype uhdas --cfgpath /home/data/AT26_17/proc/os75nb/config --ens_len 300 #--update_gbin ## python gbins: run by "run_lastensq.py" at sea # xducer_dx, xducer_dy not set ## see config/AT26_17_proc.py for other settings --skip_avg ## see above --max_search_depth 2000 --proc_engine python --incremental --find_pflags --hidedisplay --top_plotbin 1 --auto 2014-08-06 14:13:49,672 DEBUG quick_adcp sys.argv = /home/currents/programs/uhdas/scripts/run_quick.py -d os75nb 2014-08-06 14:13:49,672 DEBUG quick_adcp progdir = /home/currents/programs 2014-08-06 14:13:49,672 DEBUG quick_adcp binos = lnx 2014-08-06 14:13:49,673 DEBUG quick_setup found cruise_info.hcorr (phins, hdg, 0) 2014-08-06 14:13:49,673 INFO quick_setup reflayer: getting ref_method from dbinfo.txt 2014-08-06 14:13:49,673 INFO quick_setup reflayer: reference method = refsm 2014-08-06 14:13:49,674 INFO quick_setup reflayer: smoothed nav file is a_at_refsm.asc 2014-08-06 14:13:49,674 INFO quick_adcp importing numpy 2014-08-06 14:13:49,686 INFO quick_adcp importing matplotlib 2014-08-06 14:13:49,757 DEBUG quick_mpl in Q_mpl 2014-08-06 14:13:49,758 INFO quick_adcp ===================================================== 2014-08-06 14:13:49,758 INFO quick_adcp command line was: /home/currents/programs/uhdas/scripts/run_quick.py -d os75nb 2014-08-06 14:13:49,758 INFO quick_adcp cwd is /home/data/AT26_17/proc/os75nb 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 - lst_npings - calib - matfiles - find_pflags 2014-08-06 14:13:49,758 INFO quick_adcp original fix file is a_at.gps 2014-08-06 14:13:49,758 INFO quick_setup reflayer: ref_method already defined (refsm) 2014-08-06 14:13:49,758 INFO quick_setup reflayer: reference method = refsm 2014-08-06 14:13:49,758 INFO quick_setup reflayer: smoothed nav file is a_at_refsm.asc 2014-08-06 14:13:49,758 DEBUG quick_asect extracting matlab files for os75, nb pings 2014-08-06 14:13:49,766 DEBUG quick_setup data directory: /home/data/AT26_17/raw/os75 2014-08-06 14:13:49,767 INFO quick_setup found 266 files using wildcard expansion relative to scan directory wildcard string was: "/home/data/AT26_17/raw/os75/*.raw" 2014-08-06 14:13:49,768 DEBUG quick_setup found 266 files from original filelist 2014-08-06 14:13:49,768 DEBUG quick_adcp starting with data files (as seen from scan/ or load/ directory): /home/data/AT26_17/raw/os75/at2014_194_58241.raw ... 2014-08-06 14:13:49,768 DEBUG quick_adcp Wed Aug 6 14:13:49 2014 running quick_adcp.py as follows: --cntfile /home/data/AT26_17/proc/os75nb/os75nb_qpy.cnt ----- adcpsect variables ------ cbasename contour dbname a_at 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 2014 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 best_loggerdday_name unix_dday best_utcdday_name dday bindir /home/currents/programs/codas3/bin/lnx binos lnx btrk_step 1 cfgpath /home/data/AT26_17/proc/os75nb/config cntfile /home/data/AT26_17/proc/os75nb/os75nb_qpy.cnt commands None configtype python cruisename AT26_17 data_def vmadcp.def datadir /home/data/AT26_17/raw/os75 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 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'/home/data/AT26_17/raw/os75/at2014_217_36000.raw', '/home/data/AT26_17/raw/os75/at2014_217_43200.raw', '/home/data/AT26_17/raw/os75/at2014_217_50400.raw'] filter_hwidth 0.0208 find_pflags True firstdepth 28 fixfile a_at.gps frequency 75 gbin_style python gbindirbase /home/data/AT26_17/gbin hcorr_inst phins help False hidedisplay True incremental True instname os75 jitter 15 max_BLKprofiles 300 max_search_depth 2000 maxrunsecs None min_filter_fraction 0.5 model os nosave_editcfg 0 num_persistence 24 numbins 128 overview False pgmin 50 ping_headcorr False pingtype nb post_headcorr None printformats png proc_engine python proc_yearbase 2014 progdir /home/currents/programs py_gbindirbase /home/data/AT26_17/gbin rawstd_cutoff None ref_method refsm 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 os75nb steps2rerun timeout_secs 86400 tips False top_plotbin 1 ub_type 1920 update_gbin False use_refsm False use_smoothr False use_uvship False vardoc False varvals False wtrk_step 7 xducer_dx None xducer_dy None yearbase 2014 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 lst_npings calib matfiles find_pflags 2014-08-06 14:13:49,768 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:49,768 INFO quick_adcp step 1: set up editing files 2014-08-06 14:13:49,768 DEBUG quick_run executing commands from /home/data/AT26_17/proc/os75nb/edit 2014-08-06 14:13:49,768 DEBUG quick_run setup.m exists. not replacing 2014-08-06 14:13:49,769 DEBUG quick_run asetup.m exists. not replacing 2014-08-06 14:13:49,769 DEBUG quick_run aflagit_setup.m exists. not replacing 2014-08-06 14:13:49,769 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 2014-08-06 14:13:49,769 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:49,769 INFO quick_adcp step 2: scan files for time range 2014-08-06 14:13:49,769 INFO quick_adcp about to run numpy scan, requiring python gbins 2014-08-06 14:13:49,769 DEBUG quick_npy Starting: scanping 2014-08-06 14:13:49,954 DEBUG quick_npy Ending: scanping 2014-08-06 14:13:49,955 DEBUG quick_subs start_end_time 2014/07/14 16:10:46 to 2014/07/14 16:20:54 2014-08-06 14:13:49,955 DEBUG quick_subs dd0: 194.674144 dd1: 194.681181 2014-08-06 14:13:49,955 INFO quick_adcp in quick_adcp.py: after scan; look for database times in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:49,955 INFO quick_adcp looking for database with adcpdb/a_at*.blk 2014-08-06 14:13:49,955 INFO quick_adcp database found: listing blocks 2014-08-06 14:13:49,955 DEBUG quick_subs removing a_atdir.blk 2014-08-06 14:13:49,955 DEBUG quick_subs about to run mkblkdir 2014-08-06 14:13:49,956 DEBUG quick_subs database still exists; rerunning mkdirblk 2014-08-06 14:13:49,956 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2014-08-06 14:13:49,964 DEBUG quick_subs database passes. 2014-08-06 14:13:49,966 DEBUG quick_subs start_end_time 2014/07/14 16:15:44 to 2014/08/06 13:53:47 2014-08-06 14:13:49,966 DEBUG quick_subs dd0: 194.677593 dd1: 217.579016 2014-08-06 14:13:49,966 DEBUG quick_adcp in quick_adcp.py before load, just looked for database times 2014-08-06 14:13:49,966 DEBUG quick_adcp origdb_time_range is 2014/07/14 16:15:44 to 2014/08/06 13:53:47 2014-08-06 14:13:49,966 DEBUG quick_adcp (194.677593 to 217.579016) 2014-08-06 14:13:49,966 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:49,966 INFO quick_adcp step 3: generate averaged data... 2014-08-06 14:13:49,967 DEBUG quick_run file load/ping_editparams.txt exists. not replacing 2014-08-06 14:13:49,967 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:49,967 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/load 2014-08-06 14:13:49,967 DEBUG quick_setup running python command "run_pingavg_npy" 2014-08-06 14:13:49,967 DEBUG quick_npy Starting: pingavg 2014-08-06 14:13:49,969 DEBUG quick_npy singleping editing parameters: 2014-08-06 14:13:49,969 DEBUG quick_npy bigtarget_mab_window : 11 2014-08-06 14:13:49,969 DEBUG quick_npy rl_endbin : 20 2014-08-06 14:13:49,969 DEBUG quick_npy max_search_depth : 2000 2014-08-06 14:13:49,969 DEBUG quick_npy cor_cutoff : 120 2014-08-06 14:13:49,970 DEBUG quick_npy ampfilt : 40 2014-08-06 14:13:49,970 DEBUG quick_npy bigtarget_lgb_margin : 0.500000 2014-08-06 14:13:49,970 DEBUG quick_npy rl_startbin : 2 2014-08-06 14:13:49,970 DEBUG quick_npy ecutoff : 0.800000 2014-08-06 14:13:49,970 DEBUG quick_npy refavg_valcutoff : 1 2014-08-06 14:13:49,970 DEBUG quick_npy weakprof_percent : 30 2014-08-06 14:13:49,970 DEBUG quick_npy bigtarget_ampthresh : 55 2014-08-06 14:13:49,970 DEBUG quick_npy xducerxy is None 2014-08-06 14:13:49,976 INFO pingavg Pingavg.run for time range 217.583349 to 217.589606 2014-08-06 14:13:49,993 DEBUG pingavg Chunk 1 of 1, 217.583349 to 217.589606 2014-08-06 14:13:49,993 DEBUG pingavg Nothing written 2014-08-06 14:13:49,993 DEBUG quick_npy wrote 0 averages 2014-08-06 14:13:49,994 DEBUG quick_npy Ending: pingavg 2014-08-06 14:13:49,994 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:49,994 INFO quick_adcp step 4: load averaged data (to database) 2014-08-06 14:13:49,994 DEBUG quick_subs in del_overlapping 2014-08-06 14:13:49,994 DEBUG quick_subs lastblock: 2014-08-06 14:13:49,994 DEBUG quick_subs 22 2014-08-06 14:13:49,994 DEBUG quick_subs lastcmd: 2014-08-06 14:13:49,994 DEBUG quick_subs 22 2014-08-06 14:13:49,994 DEBUG quick_subs delblks: 2014-08-06 14:13:49,994 DEBUG quick_subs [22] 2014-08-06 14:13:49,995 DEBUG quick_subs loadblks: 2014-08-06 14:13:49,995 DEBUG quick_subs [22] 2014-08-06 14:13:49,995 DEBUG quick_subs about to run mkblkdir 2014-08-06 14:13:49,995 DEBUG quick_subs database still exists; rerunning mkdirblk 2014-08-06 14:13:49,995 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2014-08-06 14:13:50,006 DEBUG quick_subs database passes. 2014-08-06 14:13:50,006 DEBUG quick_subs start_end_time 2014/07/14 16:15:44 to 2014/08/06 07:58:48 2014-08-06 14:13:50,006 DEBUG quick_subs dd0: 194.677593 dd1: 217.332500 2014-08-06 14:13:50,006 DEBUG quick_run [22] 2014-08-06 14:13:50,006 DEBUG quick_run cmdlist 2014-08-06 14:13:50,006 DEBUG quick_run ['./ens_blk022.cmd'] 2014-08-06 14:13:50,008 INFO quick_run Warning: 1 files will be loaded; 22 already exist 2014-08-06 14:13:50,008 INFO quick_run Wed Aug 6 14:13:50 2014 2014-08-06 14:13:50,008 INFO quick_run about to load uhdas files 2014-08-06 14:13:50,008 INFO quick_run /home/data/AT26_17/raw/os75/at2014_194_58241.raw /home/data/AT26_17/raw/os75/at2014_194_64800.raw /home/data/AT26_17/raw/os75/at2014_194_72000.raw /home/data/AT26_17/raw/os75/at2014_194_78416.raw /home/data/AT26_17/raw/os75/at2014_194_79200.raw ... 2014-08-06 14:13:50,008 DEBUG quick_setup load/ldcodas.tmp exists 2014-08-06 14:13:50,008 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:50,008 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/load 2014-08-06 14:13:50,008 DEBUG quick_setup running python command "ldcodas" 2014-08-06 14:13:50,008 DEBUG quick_subs filling "thisload" timerange 2014-08-06 14:13:50,009 DEBUG quick_subs in ldcodas 2014-08-06 14:13:50,009 DEBUG quick_subs cmdlist: 2014-08-06 14:13:50,009 DEBUG quick_subs ['./ens_blk022.cmd'] 2014-08-06 14:13:50,009 DEBUG quick_subs DATABASE_NAME: ../adcpdb/a_at DEFINITION_FILE: vmadcp.def LOG_FILE: load.log YEAR_BASE: 2014 cmd_file_list /* use only if specifying cmd paths, not "@" */ END ./ens_blk022.cmd 2014-08-06 14:13:50,009 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/ldcodas ldcodas.tmp 2014-08-06 14:13:50,026 DEBUG quick_subs removing a_atdir.blk 2014-08-06 14:13:50,027 DEBUG quick_subs about to run mkblkdir 2014-08-06 14:13:50,027 DEBUG quick_subs database still exists; rerunning mkdirblk 2014-08-06 14:13:50,027 DEBUG quick_subs running /home/currents/programs/codas3/bin/lnx/mkblkdir mkblkdir.tmp 2014-08-06 14:13:50,038 DEBUG quick_subs database passes. 2014-08-06 14:13:50,039 DEBUG quick_subs start_end_time 2014/07/14 16:15:44 to 2014/08/06 14:08:46 2014-08-06 14:13:50,039 DEBUG quick_subs dd0: 194.677593 dd1: 217.589421 2014-08-06 14:13:50,039 INFO quick_adcp --------------------- 2014-08-06 14:13:50,039 INFO quick_adcp loaded_time_range is 2014/07/14 16:15:44 to 2014/08/06 14:08:46 2014-08-06 14:13:50,039 INFO quick_adcp (194.677593 to 217.589421) 2014-08-06 14:13:50,040 INFO quick_adcp origdb_time_range is 2014/07/14 16:15:44 to 2014/08/06 13:53:47 2014-08-06 14:13:50,040 INFO quick_adcp (194.677593 to 217.579016) 2014-08-06 14:13:50,040 INFO quick_adcp thisload_time_range is 2014/08/06 08:03:47 to 2014/08/06 14:08:46 2014-08-06 14:13:50,040 INFO quick_adcp (217.335961 to 217.335961) 2014-08-06 14:13:50,040 INFO quick_adcp --------------------- 2014-08-06 14:13:50,040 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:50,040 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/adcpdb 2014-08-06 14:13:50,040 DEBUG quick_setup running python command "lst_conf" 2014-08-06 14:13:50,040 DEBUG quick_subs dbname: a_at output: a_at.cnh time_ranges: all 2014-08-06 14:13:50,041 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_conf lst_conf.tmp 2014-08-06 14:13:51,352 DEBUG quick_setup found (in edit/asetup.m): 2014-08-06 14:13:51,352 DEBUG quick_setup config.beamangle is 30 2014-08-06 14:13:51,352 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:51,352 INFO quick_adcp step 5: set up files for gautoedit.py 2014-08-06 14:13:51,352 DEBUG quick_run file edit/codas_editparams.txt exists. not replacing 2014-08-06 14:13:51,352 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:51,353 INFO quick_adcp step 6: set up files for gautoedit.py 2014-08-06 14:13:51,353 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:51,353 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/edit 2014-08-06 14:13:51,353 DEBUG quick_setup running python command "setflags" 2014-08-06 14:13:51,353 DEBUG quick_subs dbname: ../adcpdb/a_at pg_min: 50 set_range_bit time_ranges: all 2014-08-06 14:13:51,353 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/setflags setflags.tmp 2014-08-06 14:13:51,378 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:51,378 INFO quick_adcp step 7: get navigation 2014-08-06 14:13:51,378 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:51,378 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/nav 2014-08-06 14:13:51,378 DEBUG quick_setup running python command "catnav" 2014-08-06 14:13:51,382 DEBUG quick_setup cal/rotate/lst_hdg.tmp exists 2014-08-06 14:13:51,382 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:51,382 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/cal/rotate 2014-08-06 14:13:51,382 DEBUG quick_setup running python command "lst_hdg" 2014-08-06 14:13:51,382 DEBUG quick_subs dbname: ../../adcpdb/a_at output: scn.hdg step_size= 1 year_base= 2014 time_ranges: all 2014-08-06 14:13:51,382 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_hdg lst_hdg.tmp 2014-08-06 14:13:51,403 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:51,403 INFO quick_adcp step 8: get heading correction 2014-08-06 14:13:51,404 DEBUG quick_run hcorr_inst is phins 2014-08-06 14:13:51,404 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:51,404 INFO quick_adcp step 9: rotate velocities 2014-08-06 14:13:51,404 DEBUG quick_setup cal/rotate/norotate.tmp exists 2014-08-06 14:13:51,404 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:51,404 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/cal/rotate 2014-08-06 14:13:51,404 DEBUG quick_setup running python command "norotate" 2014-08-06 14:13:51,404 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: 2014/07/14 16:15:44 to 2014/08/06 14:08:46 OPTION_LIST: water_and_bottom_track: year_base= 2014 /* time_angle_file: time_angle.ang */ amplitude= 1.0 angle_0= 0.0 end end 2014-08-06 14:13:51,404 DEBUG quick_setup about to run echo "writing dummy rotate file" 2014-08-06 14:13:51,407 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:51,407 INFO quick_adcp step 10: nav steps: run adcpsect 2014-08-06 14:13:51,407 DEBUG quick_setup nav/as_nav.tmp exists 2014-08-06 14:13:51,408 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:51,408 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/nav 2014-08-06 14:13:51,408 DEBUG quick_setup running python command "as_nav" 2014-08-06 14:13:51,408 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at step_size: 1 ndepth: 20 time_ranges: separate year_base= 2014 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 2014/07/14 16:15:44 to 2014/08/06 14:08:46 /* the whole time range */ 2014-08-06 14:13:51,408 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2014-08-06 14:13:51,448 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:51,448 INFO quick_adcp step 11: nav steps: run refabs 2014-08-06 14:13:51,448 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:51,448 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/nav 2014-08-06 14:13:51,448 DEBUG quick_setup running python command "refabs" 2014-08-06 14:13:51,449 DEBUG quick_subs fix_file_type: simple reference_file: a_at.nav fix_file: a_at.gps output: a_at.ref year_base= 2014 ensemble_length= 300 gap_tolerance= 10 2014-08-06 14:13:51,449 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabs refabs.tmp 2014-08-06 14:13:51,490 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:51,491 INFO quick_adcp step 12: nav steps: run smoothr for plots 2014-08-06 14:13:51,491 DEBUG quick_setup nav/smoothr.tmp exists 2014-08-06 14:13:51,491 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:51,491 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/nav 2014-08-06 14:13:51,491 DEBUG quick_setup running python command "smoothr" 2014-08-06 14:13:51,491 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 2014-08-06 14:13:51,492 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/smoothr smoothr.tmp 2014-08-06 14:13:51,649 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:51,650 INFO quick_adcp step 13: nav steps: smooth navigation 2014-08-06 14:13:51,650 INFO quick_adcp about to run numpy reflayer smoothing, method=refsm 2014-08-06 14:13:51,650 DEBUG quick_npy Starting: refsm 2014-08-06 14:13:51,745 DEBUG nav dtmin = -0.50 dtmax = 0.50 2014-08-06 14:13:51,834 DEBUG quick_npy Ending: refsm 2014-08-06 14:13:51,834 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:51,834 INFO quick_adcp step 14: nav steps: put smoothed nav into codasdb 2014-08-06 14:13:51,834 DEBUG quick_setup nav/putnav.tmp exists 2014-08-06 14:13:51,834 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:51,834 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/nav 2014-08-06 14:13:51,834 DEBUG quick_setup running python command "putnav" 2014-08-06 14:13:51,834 DEBUG quick_subs dbname: ../adcpdb/a_at position_file: a_at_refsm.asc year_base= 2014 tolerance= 5 navigation_sources: gps end 2014-08-06 14:13:51,834 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/putnav putnav.tmp 2014-08-06 14:13:51,884 INFO quick_adcp plotting navigation 2014-08-06 14:13:51,884 DEBUG quick_mpl Starting plot: nav 2014-08-06 14:13:52,148 DEBUG quick_mpl Ending plot: nav 2014-08-06 14:13:52,148 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:52,148 INFO quick_adcp step 15: nav steps: make reflayer plots 2014-08-06 14:13:52,148 DEBUG quick_mpl Starting plot: refl 2014-08-06 14:13:52,264 DEBUG quick_mplplots found 22.852814 days of data 2014-08-06 14:13:52,264 DEBUG quick_mplplots start day is 194.000000 2014-08-06 14:13:52,264 DEBUG quick_mplplots figures with 2.000000 days per page 2014-08-06 14:13:52,265 DEBUG quick_mplplots printing 12 pages 2014-08-06 14:13:52,265 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2014-08-06 14:13:52,746 DEBUG quick_mpl Ending plot: refl 2014-08-06 14:13:52,746 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:52,746 INFO quick_adcp step 16: find profile flags 2014-08-06 14:13:52,746 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:52,746 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/edit 2014-08-06 14:13:52,746 DEBUG quick_setup running python command "run_autoedit_npy" 2014-08-06 14:13:52,746 DEBUG quick_npy Starting: autoedit 2014-08-06 14:13:52,847 DEBUG pingedit wrote 1 bad bins to abadbin_tmp.asc 2014-08-06 14:13:52,858 DEBUG pingedit wrote 1 bad profiles to abadprf_tmp.asc 2014-08-06 14:13:52,858 DEBUG quick_npy Ending: autoedit 2014-08-06 14:13:52,858 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:52,858 INFO quick_adcp step 17: apply editing 2014-08-06 14:13:52,858 DEBUG quick_run starting in: /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:52,858 DEBUG quick_run executing commands from: edit 2014-08-06 14:13:52,859 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/dbupdate ../adcpdb/a_at abadprf_tmp.asc 2014-08-06 14:13:52,864 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/badbin ../adcpdb/a_at abadbin_tmp.asc 2014-08-06 14:13:52,871 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/set_lgb ../adcpdb/a_at 30 2014-08-06 14:13:52,878 DEBUG quick_subs dbname: ../adcpdb/a_at pg_min: 50 set_range_bit time_ranges: all 2014-08-06 14:13:52,878 DEBUG quick_run about to run /home/currents/programs/codas3/bin/lnx/setflags setflags.tmp 2014-08-06 14:13:52,910 DEBUG quick_run changing directories back to /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:52,910 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:52,910 INFO quick_adcp step 18: run nav steps 2014-08-06 14:13:52,910 DEBUG quick_setup nav/as_nav.tmp exists 2014-08-06 14:13:52,910 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:52,911 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/nav 2014-08-06 14:13:52,911 DEBUG quick_setup running python command "as_nav" 2014-08-06 14:13:52,911 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at step_size: 1 ndepth: 20 time_ranges: separate year_base= 2014 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 2014/07/14 16:15:44 to 2014/08/06 14:08:46 /* the whole time range */ 2014-08-06 14:13:52,911 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2014-08-06 14:13:52,953 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:52,954 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/nav 2014-08-06 14:13:52,954 DEBUG quick_setup running python command "refabs" 2014-08-06 14:13:52,954 DEBUG quick_subs fix_file_type: simple reference_file: a_at.nav fix_file: a_at.gps output: a_at.ref year_base= 2014 ensemble_length= 300 gap_tolerance= 10 2014-08-06 14:13:52,954 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabs refabs.tmp 2014-08-06 14:13:53,000 DEBUG quick_setup nav/smoothr.tmp exists 2014-08-06 14:13:53,000 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:53,000 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/nav 2014-08-06 14:13:53,001 DEBUG quick_setup running python command "smoothr" 2014-08-06 14:13:53,001 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 2014-08-06 14:13:53,001 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/smoothr smoothr.tmp 2014-08-06 14:13:53,169 DEBUG quick_setup nav/putnav.tmp exists 2014-08-06 14:13:53,169 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:53,169 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/nav 2014-08-06 14:13:53,169 DEBUG quick_setup running python command "putnav" 2014-08-06 14:13:53,170 DEBUG quick_subs dbname: ../adcpdb/a_at position_file: a_at_refsm.asc year_base= 2014 tolerance= 5 navigation_sources: gps end 2014-08-06 14:13:53,170 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/putnav putnav.tmp 2014-08-06 14:13:53,224 DEBUG quick_mpl Starting plot: nav 2014-08-06 14:13:53,505 DEBUG quick_mpl Ending plot: nav 2014-08-06 14:13:53,505 DEBUG quick_mpl Starting plot: refl 2014-08-06 14:13:53,625 DEBUG quick_mplplots found 22.852814 days of data 2014-08-06 14:13:53,626 DEBUG quick_mplplots start day is 194.000000 2014-08-06 14:13:53,626 DEBUG quick_mplplots figures with 2.000000 days per page 2014-08-06 14:13:53,626 DEBUG quick_mplplots printing 12 pages 2014-08-06 14:13:53,626 DEBUG quick_mplplots yrange will be [1.000000, 1.000000] 2014-08-06 14:13:54,133 DEBUG quick_mpl Ending plot: refl 2014-08-06 14:13:54,133 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:54,134 INFO quick_adcp step 19: plot temperature 2014-08-06 14:13:54,134 DEBUG quick_setup edit/lst_temp.tmp exists 2014-08-06 14:13:54,134 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:54,134 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/edit 2014-08-06 14:13:54,134 DEBUG quick_setup running python command "lst_temp" 2014-08-06 14:13:54,134 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at.tem step_size= 1 year_base= 2014 time_ranges: all 2014-08-06 14:13:54,134 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_temp lst_temp.tmp 2014-08-06 14:13:54,167 DEBUG quick_mpl Starting plot: temp 2014-08-06 14:13:54,215 DEBUG quick_mplplots plotting 6307 points 2014-08-06 14:13:54,388 DEBUG quick_mpl Ending plot: temp 2014-08-06 14:13:54,388 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:54,388 INFO quick_adcp step 20: plot numper of pings per ensemble 2014-08-06 14:13:54,388 DEBUG quick_setup edit/lst_npings.tmp exists 2014-08-06 14:13:54,388 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:54,388 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/edit 2014-08-06 14:13:54,388 DEBUG quick_setup running python command "lst_npings" 2014-08-06 14:13:54,388 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at_npings.txt step_size= 1 year_base= 2014 time_ranges: all 2014-08-06 14:13:54,389 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_npings lst_npings.tmp 2014-08-06 14:13:54,417 DEBUG quick_mpl Starting plot: npings 2014-08-06 14:13:54,461 DEBUG quick_mplplots plotting 6307 points 2014-08-06 14:13:54,580 DEBUG quick_mpl Ending plot: npings 2014-08-06 14:13:54,580 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:54,580 INFO quick_adcp step 21: run calibration steps 2014-08-06 14:13:54,580 DEBUG quick_setup cal/botmtrk/lst_btrk.tmp exists 2014-08-06 14:13:54,580 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:54,581 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/cal/botmtrk 2014-08-06 14:13:54,581 DEBUG quick_setup running python command "lst_btrk" 2014-08-06 14:13:54,581 DEBUG quick_subs dbname: ../../adcpdb/a_at output: a_at.btm step_size= 1 year_base= 2014 time_ranges: 2014/07/14 16:15:44 to 2014/08/06 14:08:46 /* whole time range */ 2014-08-06 14:13:54,581 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/lst_btrk lst_btrk.tmp 2014-08-06 14:13:54,597 DEBUG quick_setup cal/botmtrk/refabsbt.tmp exists 2014-08-06 14:13:54,597 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:54,597 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/cal/botmtrk 2014-08-06 14:13:54,598 DEBUG quick_setup running python command "refabsbt" 2014-08-06 14:13:54,598 DEBUG quick_subs fix_file_type: simple reference_file: a_at.btm fix_file: ../../nav/a_at.gps output: a_at.ref year_base= 2014 ensemble_length= 300 gap_tolerance= 60 2014-08-06 14:13:54,598 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/refabsbt refabsbt.tmp 2014-08-06 14:13:54,604 DEBUG quick_mpl Starting plot: btcal 2014-08-06 14:13:54,957 DEBUG quick_mpl Ending plot: btcal 2014-08-06 14:13:54,957 DEBUG quick_setup nav/as_nav.tmp exists 2014-08-06 14:13:54,957 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:54,957 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/nav 2014-08-06 14:13:54,957 DEBUG quick_setup running python command "as_nav" 2014-08-06 14:13:54,957 DEBUG quick_subs dbname: ../adcpdb/a_at output: a_at step_size: 1 ndepth: 20 time_ranges: separate year_base= 2014 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 2014/07/14 16:15:44 to 2014/08/06 14:08:46 /* the whole time range */ 2014-08-06 14:13:54,957 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_nav.tmp 2014-08-06 14:13:55,001 DEBUG quick_setup cal/watertrk/timslip.tmp exists 2014-08-06 14:13:55,001 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:55,001 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/cal/watertrk 2014-08-06 14:13:55,001 DEBUG quick_setup running python command "timslip" 2014-08-06 14:13:55,002 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= 2014 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 2014-08-06 14:13:55,002 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timslip timslip.tmp 2014-08-06 14:13:55,021 DEBUG quick_mpl Starting plot: wtcal 2014-08-06 14:13:55,023 DEBUG quick_mplplots Found 17 calibration points 2014-08-06 14:13:55,592 DEBUG quick_mpl Ending plot: wtcal 2014-08-06 14:13:55,592 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:55,592 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/cal/watertrk 2014-08-06 14:13:55,593 DEBUG quick_setup running python command "run_guess_xducerxy_npy" 2014-08-06 14:13:55,593 DEBUG quick_npy Starting: guess_xducerxy 2014-08-06 14:13:55,693 DEBUG quick_npy Ending: guess_xducerxy 2014-08-06 14:13:55,693 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:55,693 INFO quick_adcp step 22: extract matlab "allbins" 2014-08-06 14:13:55,693 DEBUG quick_asect ------------ step 18: make matlab files for plotting ------------- 2014-08-06 14:13:55,693 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:55,693 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/vector 2014-08-06 14:13:55,693 DEBUG quick_setup running python command "timegrid" 2014-08-06 14:13:55,693 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timegrid a_at.tmp 2014-08-06 14:13:55,702 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:55,702 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/vector 2014-08-06 14:13:55,702 DEBUG quick_setup running python command "as_vect" 2014-08-06 14:13:55,702 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_vect.tmp 2014-08-06 14:13:55,781 DEBUG quick_asect done making vector matfiles 2014-08-06 14:13:55,782 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:55,782 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/contour 2014-08-06 14:13:55,782 DEBUG quick_setup running python command "timegrid" 2014-08-06 14:13:55,782 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/timegrid a_at.tmp 2014-08-06 14:13:55,793 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:55,793 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/contour 2014-08-06 14:13:55,793 DEBUG quick_setup running python command "as_cont" 2014-08-06 14:13:55,793 DEBUG quick_setup about to run /home/currents/programs/codas3/bin/lnx/adcpsect as_cont.tmp 2014-08-06 14:13:55,903 DEBUG quick_setup starting in /home/data/AT26_17/proc/os75nb 2014-08-06 14:13:55,904 DEBUG quick_setup executing commands from /home/data/AT26_17/proc/os75nb/contour 2014-08-06 14:13:55,904 DEBUG quick_setup about to run getmat -qrs -f allbins_ ../adcpdb/a_at 2014-08-06 14:13:56,097 DEBUG quick_asect done running getmat with "allbins" 2014-08-06 14:13:56,097 INFO quick_adcp --------------------------------------------- 2014-08-06 14:13:56,097 INFO quick_adcp step 23: write "cruise_info.txt" 2014-08-06 14:13:56,115 INFO root copying NOFIG to /home/adcp/www/figures/os75nb_hcorr_plot.png 2014-08-06 14:13:56,115 INFO root copying NOFIG to /home/adcp/www/figures/thumbnails/os75nb_hcorr_plot_thumb.png 2014-08-06 14:13:56,115 DEBUG root matfile is contour/contour_uv.mat 2014-08-06 14:13:56,118 INFO root copying contour/contour_uv.mat to /home/adcp/www/data/os75nb_cont_uv.mat 2014-08-06 14:13:56,118 DEBUG root matfile is vector/vector_uv.mat 2014-08-06 14:13:56,119 INFO root copying vector/vector_uv.mat to /home/adcp/www/data/os75nb_vect_uv.mat 2014-08-06 14:13:56,119 DEBUG root matfile is contour/contour_xy.mat 2014-08-06 14:13:56,119 INFO root copying contour/contour_xy.mat to /home/adcp/www/data/os75nb_cont_xy.mat 2014-08-06 14:13:56,119 DEBUG root matfile is vector/vector_xy.mat 2014-08-06 14:13:56,119 INFO root copying vector/vector_xy.mat to /home/adcp/www/data/os75nb_vect_xy.mat 2014-08-06 14:13:56,119 DEBUG root about to copy file edit/a_at.tem to /home/adcp/www/data/os75nb_temp.asc 2014-08-06 14:13:56,120 INFO root copying edit/a_at.tem to /home/adcp/www/data/os75nb_temp.asc 2014-08-06 14:13:56,121 INFO netcdf Using pupynere. 2014-08-06 14:13:56,246 DEBUG root about to copy netcdf file /home/data/AT26_17/proc/os75nb/contour/os75nb.nc to /home/adcp/www/data/os75nb.nc 2014-08-06 14:13:56,254 INFO root copying edit/a_at.tem to /home/adcp/www/data/os75nb.nc 2014-08-06 14:13:56,272 INFO root generating pingstats for os75nb 2014-08-06 14:13:56,272 INFO root Ending quick_adcp.py