.. _commandline-tools:

Command-line tools for UHDAS data
++++++++++++++++++++++++++++++++++

These tools require the full Python CODAS installation.
In all cases, you will need to type the name with ``--help``
to get more information about usage.

Some of these are pretty simple, some are more sophisticated.

General purpose
^^^^^^^^^^^^^^^^^^

**figview.py**: view a collection of files, eg:

     -  ``figview.py``: view all PNG files in all subdirectories
         of current working directory
     -  ``figview.py dirname`` : view all PNG files in subdirectories of "dirname"
     -  ``figview.py *.png`` : view all PNG files in the current directory


**txyselect.py**: select start/end sections for dday,lon,lat  eg:

     - ``txyselect.py nav/dbname.gps``
     - This program is used for section selection in ``quick_web`` (see below)
     - Guidelines for choosing sections are :ref:`here <quick_web>`


**to_day**:

     - convert YYYY/MM/DD hh:mm:ss time to CODAS decimal day (relative to YEARBASE), eg::

               to_day 1970    2015 5 18 8 30 00
               to_day 2015    2015 5 18 8 30 00

**to_date**:

     - convert CODAS decimal day (relative to a yearbase) into YYYY/MM/DD hh:mm:ss::

               to_date 2015 137.354



Explore CODAS data
^^^^^^^^^^^^^^^^^^^

**plot_nav.py** : plot lon, lat over topography, eg:

     - ``plot_nav.py nav/aship.gps``

**quick_mplplots.py**: update processing directory with png figures (NOTE:
If the processing directory is old, additional information may be necessary.

     - ``quick_mplplots.py --yearbase YYYY --all``

**dataviewer.py** Use in one of :ref:`four modes <dataviewer-index>`:

     - ``dataviewer.py`` : CODAS data viewer

     - ``dataviewer.py -c`` : compare two CODAS databases (same cruise)

     - ``dataviewer.py -e``: edit a codas database
          + call from ``edit`` directory
          + same as ``gautoedit.py``

     - ``dataviewer.py -p`` : view singleping data as well
          + call from ``edit`` directory
          + assumes processing directory is correctly configured
            for full Python Processing, including the
            existence of the raw data and rbin files

**plot_reflayer.py**: compare phase and amplitude between 2 CODAS datasets


Overview of datasets
^^^^^^^^^^^^^^^^^^^^^^^^^^

**vmdas_info.py**

    - print out some useful information about VmDAS files

**uhdas_info.py**

    - print out some useful information about a UHDAS dataset


UHDAS serial data
^^^^^^^^^^^^^^^^^^^^^^

**showlast.py**

    - list recent raw, rbin, gbin files, or lines from raw files

**plot_rbins.py**

    - plot 1-2 serial feeds (rbin files). If feeds
      have the same fields, plot the difference.
      Longitude and latitude diffs are plotted in meters

**plot_rnav.py**

    - plot rbin positions over topography

**plot_pashr.py**:

     - plot $PASHR heading accuracy from a collection of rbins

**plot_posmv.py**:

     - plot $PASHR heading accuracy from a UHDAS dataset

**plot_hbins.py**:

     - plot all configured heading devices from a UHDAS directory

Raw ADCP data
^^^^^^^^^^^^^


**plot_rawadcp.py**

    - plot 4 beams of raw adcp data: (velocity, amplitude or correlation)

**EA_estimator.py**

    - estimate the transducer angle relative to the bow of the ship
      from beam-coordinates data (UHDAS ``*.raw`` or VmDAS ``*.ENR``)



CODAS processing: fixing holes in heading correction
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

**patch_hcorr.py**

    - run from cal/rotate
    - ``patch_hcorr.py --help`` has extensive help
    - summary:
             + read ens_hcorr.asc
             + plot heading correction, stddev, number of pts
             + gives graphical access to filtering options
             + allows manual editing
             + interpolate through holes
             + write new (patched) file and make figures
             + print instructions to use the new file

 For more detail about **patch_hcorr.py**, click :ref:`here <patch_hcorr>`



CODAS processing: horizontal GPS and ADCP separation ("dxdy")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

For more detail about **ADCP Transducer-GPS offset** (maneuvering),
click  :ref:`here <xducer_dxdy>` .


CODAS processing: poor PG causes underway bias ("uvship")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

For more detail about this experimental algorpthm to sometimes fix
**alongtrack biases caused by pervasive bad Percent Good**,
click  :ref:`here <uvship>` . NOTE that this algorithm requires
a stable GPS feed and that the dxdy algorithm (above) already
have been applied at the single-ping stage.


CODAS processing: make a web site
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

**quick_web.py**

    - creates web pages like `each of these
      <https://currents.soest.hawaii.edu/go-ship/sadcp/list_n_map_view/cruises/1/index.html>`_ (one for
      each ADCP)
    - manually select sections:  ``quick_web.py --interactive``
    - can also run with automated settings
    - uses ``txyselect.py`` for section selection

Guidelines for choosing sections are  :ref:`here <quick_web>`


CODAS processing setup (advanced)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

**link_uhdaslegs.py**

    - link files from multiple legs (OSX,linux)

**mk_rbin.py**

    -  remake rbins (gets most of them; do the rest manually
       with **asc2bin.py** or **serasc2bin.py**.
       (more information about rbin messages is
       :ref:`here<regenerate_uhdas>`



.. toctree::
   :maxdepth: 1
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