Processing Ocean Surveyor data with sequential use of one pingtypeΒΆ

This is a work in progress.

There is a  script that should help automate the processing
of cruises where only one pingtype is used at a time,
but it could be one or the other.  For example

    - bb over the shelf
    - nb over the deep
    - bb over the shelf

  Getting Ready:

Make sure you are running a recent version of CODAS processing.
See documentation about upgrading, or switching to a new virtual computer


(1) set up for ENR processing as discussed in the workshop (and docs)
(2) assumes:
    *  control file is called "q_py.cnt"
    *  "--update_gbins" is in the control file or gbins are already new
    *  in q_py.cnt: this option  "--sonar os75bb" or "--sonar os75nb"
       should be commented: we are going to specify it in the command line
       (because we will be choosing different pingtypes for different
    chunks of data): like this in q_py.cnt:

#      --sonar       ## COMMENT THIS OUT -- put in command-line

(3) The script will create the set of commands that will get you a
    dataset with
     *  the only pingtype that exists, if the data are not inverleaved
     *  the default specified, if the data are interleaved

   eg: from the processing directory (created by "adcptree.py")

   For the Oleander data (example above) which has
    - bb over the shelf
    - nb over the deep
    - bb over the shelf

     list_qpy_chunks.py  os75 ../fake_uhdas_data/Oleander_Nov2011/raw/os75/*raw

    If you had interleaved pings, you would have to pick a default
    (preferred) ping type using the "--pingpref" option:

     list_qpy_chunks.py  --pingpref nb ../fake_uhdas_data/Oleander_Nov2011/raw/os75/*raw

(5) output is below.  The idea is to actually dump this list of commands in a
    file and then "source" the file (to run all the commands)


     list_qpy_chunks.py  --pingpref nb ../fake_uhdas_data/Oleander_Nov2011/raw/os75/*raw > run_quick.s
     source run_quick.s

    NOTE: the same output will be generated if you point to the vmdas_data (ENR, STA)
    or the fake_uhdas_data (*.raw) because it is looking at configuration changes
    not just file boundaries.

quick_adcp.py --cntfile q_py.cnt --sonar os75bb --incremental  --dday_bailout 314.68842 --auto
quick_adcp.py --cntfile q_py.cnt --sonar os75bb --incremental  --dday_bailout 314.87945 --auto
quick_adcp.py --cntfile q_py.cnt --sonar os75bb --incremental  --dday_bailout 315.04602 --auto
quick_adcp.py --cntfile q_py.cnt --sonar os75nb --incremental  --dday_bailout 320.16733 --auto
quick_adcp.py --cntfile q_py.cnt --sonar os75bb --incremental  --dday_bailout 320.37591 --auto
quick_adcp.py --cntfile q_py.cnt --sonar os75bb --incremental  --dday_bailout 320.57815 --auto
quick_adcp.py --cntfile q_py.cnt --sonar os75bb --incremental  --dday_bailout 320.61893 --auto

The two switches "--incremental" and "-dday_bailout" work together.
      "--incremental" allows pieces to be added later
      "--dday_bailout xxx" quits processing at the specified time

This is a specific use case.

written 2015/04/20; this strategy is still valid, though not tested of late.
Email us if you have a question.