Aug 2014
--------


==============================  quick_adcp.py -- Python processing steps ===================================|====================================


step     | working directory |  description           |    run                    |  input file(s)          ||  output file(s)
*****    | ***************   |  ******************    |  ****************         |  ********************** ||  *********************************
setup    | (various)         |  set up editing files  |    (various)              |                         ||
=====    | ===============   |  ===================   |   ================        |  ====================== ||  =================================
gbins    |  load             |  generate gbins        |   Pygbin_script.py        |                         ||  gbins (in UHDAS dir)
=====    | ===============   |  ===================   |   ================        |  ====================== ||  =================================
scan     |  scan             |  get time ranges       |   Scanping_script.py      |                         ||  dbname.scn
=====    | ===============   |  ===================   |   ================        |  ====================== ||  =================================
load(1)  |  load             |  make averages         |   PingAverage_script.py   |                         ||  ens*.cmd, ens*.bin (always)
         |                   |                        |                           |  xducer_dx,xducer_dy==0 ||  ens*.gps2  (original positions)
         |                   |                        |                           |  xducer_dx,xducer_dy!=0 ||  ens*.gpst2 (translated positions)
-----    | ---------------   |  ------------------    |  ----------------         |  ---------------------- ||  ---------------------------------
load(2)  |  load             |  load averages         |      ldcodas              |        ldcodas.tmp      ||  fills codas database
=====    | ===============   |  ===================   |   ================        |  ====================== ||  =================================
setup    |  edit             |  set up edit defaults  |   (various)               |                         ||
=====    | ===============   |  ===================   |   ================        |  ====================== ||  =================================
cat nav  |  nav              |  cat navigation        |   cat ../load/*gps2       |                         ||  aship.gps
         |                   |                        |   cat ../load/*gpst2      |                         ||  aship.agt (only if ../load/*gpst2)
=====    | ===============   |  ===================   |   ================        |  ====================== ||  =================================
hcorr    |  cal/rotate       |  make hcorr plots      |   Hcorrplot_script.py     |     ens_hcorr.asc       ||  hcorr_mpl_*.png


    ***** below this are steps typically run more than once, run with --steps2rerun ******

step     | working directory | description            |    run                    |  input file(s)          ||  output file(s)
*****    | ***************   | ******************     |  ****************         |  ********************** ||  *********************************
rotate   |  cal/rotate       | rotate velocities      |   rotate                  |        rotate.tmp       ||   rotate.log
=====    | ===============   | ===================    |   ================        |  ====================== ||  =================================
navsteps |                   | (reflayer plots)       |                           |                         ||
         |   nav             | extract uship,vship    |   adcpsect                |     as_nav.tmp          ||  aship.nav
         |   nav             | extract reflayer       |   refabs                  |     refabs.tmp          ||  aship.ref
         |   nav             | run smoothr            |   smoothr                 |     smoothr.tmp         ||  aship.sm
         |   nav             | reflayer plots         |   Refplot_script.py       |                         ||  reflayer*.png
-----    | ---------------   | ------------------     |  ----------------         |  ---------------------- ||  ---------------------------------
(note)   |   nav             | --ref_method smoothr   |   smoothr                 |   aship.nav, aship.ref  ||  aship_refsm.asc
(note)   |   nav             |                        |   putnav                  |   aship_refsm.asc       ||  (changes database)
-----    | ---------------   | ------------------     |  ----------------         |  ---------------------- ||  ---------------------------------
         |                   | smoothing navigation   |                           |                         ||
(note)   |   nav             | --ref_method refsm     |   Refsm_script.py         |  aship.gps (aship.agt)  ||  refuv.asc
(note)   |   nav             | --refuv_source nav     |   put_txy                 |  aship.gps (aship.agt)  ||  (changes database)
(note)   |   nav             |                        |   put_tuv                 |  refuv.asc              ||  (changes database)
-----    | ---------------   | ------------------     |  ----------------         |  ---------------------- ||  ---------------------------------
         |                   | smoothing navigation   |                           |                         ||
(note)   |   nav             | --ref_method refsm     |   Refsm_script.py         |  aship.gps (aship.agt)  ||  refuv.asc
(note)   |   nav             | --refuv_source uvship  |   put_txy                 |  aship.gps (aship.agt)  ||  (changes database)
(note)   |   nav             |                        |   put_tuv                 |  refuv.asc              ||  (changes database)
-----    | ---------------   | ------------------     |  ----------------         |  ---------------------- ||  ---------------------------------
         |   nav             | plot navigation        |   Navplot_script.py       |                         ||  nav_plot.png
=====    | ===============   | ===================    |   ================        |  ====================== ||  =================================
plots    |  edit             | plot temperature       |   Tempplot_script.py      |                         ||  aship.tem, temp_plot.png
-----    | ---------------   | ------------------     |  ----------------         |  ---------------------- ||  ---------------------------------
plots    |  edit             | plot num pings         |   NPingplot_script.py     |                         ||  nping_plot.png
=====    | ===============   | ===================    |   ================        |  ====================== ||  =================================
wtcal    |  cal/watertrk     | watertrack cal         |                           |                         ||
         |                   |                        |   timslip                 |    timslip.tmp,         ||
         |                   |                        |                           |   ../../nav/dbname.nav  ||  aship.cal
         |                   |                        |   Wtplot_script.py        |     aship.cal           ||  adcpcal.out, wtcal_edited
=====    | ===============   | ==================     |  ================         |  ====================== ||  =================================
xducerxy |  cal/watertrk     | transducer=gps offset  |   Guess_Xducerxy_script.py|                         ||  guess_xducerxy.out
=====    | ===============   | ==================     |  ================         |  ====================== ||  =================================
btcal    |  cal/botmtrk      | bottomtrack cal        |   lstbtrk                 |    lstbtrk.tmp          ||  aship.btm
         |                   |                        |   refabsbt                |    aship.btm,           ||
         |                   |                        |                           |     ../../nav/aship.gps ||    aship.ref
         |                   |                        |   Btplot_script.py        |    btcaluv.out          ||
=====    | ===============   | ==================     |  ================         |  ====================== ||  =================================
matfiles |  vector           | vector matfiles        |   timegrid                |    aship.tmp            ||  aship.tmg
         |                   |                        |   adcpsect                |    aship.tmg            ||  vector_uv.mat, vector_xy.mat
-----    | ---------------   | ------------------     |  ----------------         |  ---------------------- ||  ---------------------------------
matfiles |  contour          | contour matfiles       |   timegrid                |    aship.tmp            ||  aship.tmg
         |                   |                        |   adcpsect                |    aship.tmg            ||  contour_uv.mat, contour_xy.mat
-----    | ---------------   | ------------------     |  ----------------         |  ---------------------- ||  ---------------------------------
matfiles |  contour          | all bins               |   getmat                  |                         ||  allbins_*.mat
=====    | ==============    | ==================     |  ================         |  ====================== ||  =================================
info     |   ./              | cruise metadata        |                           |                         ||  cruise_info.txt
-----    | ---------------   | ------------------     |  ----------------         |  ---------------------- ||  ---------------------------------
info     |   ./              | processing info        |                           |                         ||  dbinfo.txt
=====    | ===============   | ==================     |  ================         |  ====================== ||  =================================



(note): see uvship.txt