Processing data with runots.py
******************************

Data are processed using the umbrella run script ``runots.py``. With this script the user specifies the instrument and step to be applied to the data.

For most instruments, this is a two-step process:

1. instrument data to raw CDF
2. raw CDF to clean .nc

For some instruments (usually those measuring waves) there is a third step:

3. clean .nc to wave-statistics .nc

The user will call ``runots.py`` from the command line, with arguments described below. The autogenerated documentation below can be a little challenging to interpret, so here's an example:

``runots.py aqd hdr2cdf gatts_file.txt config_file.yaml``

The above command specifies ``aqd`` (Aquadopp collecting in currents mode) and ``hdr2cdf`` (step 1 above, instrument data to raw CDF), using the specified :doc:`configuration files </config>`.

To get to the final .nc file, the user would then run ``runots.py aqd cdf2nc raw_cdf_file_name.cdf``

To get final wave-statistics .nc files for supported instruments, the user has 2 potential options ``nc2waves`` and ``nc2diwasp`` with a clean .nc file of continuous or burst data as a positional argument

To find out what options are available for a specific instrument the user can run ``runots.py <insert instrument code> -h``
   

runots.py
---------

.. argparse::
   :ref: stglib.core.cmd.runots_parser
   :prog: runots.py