pyglider.slocum
===============

.. py:module:: pyglider.slocum

.. autoapi-nested-parse::

   Routines to convert raw slocum dinkum files to netcdf timeseries.

   ..
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Functions
---------

.. autoapisummary::

   pyglider.slocum.binary_to_rawnc
   pyglider.slocum.merge_rawnc
   pyglider.slocum.raw_to_timeseries
   pyglider.slocum.parse_gliderState
   pyglider.slocum.parse_logfiles


Module Contents
---------------

.. py:function:: binary_to_rawnc(indir, outdir, cacdir, sensorlist, deploymentyaml, incremental=True, scisuffix='EBD', glidersuffix='DBD')

   
   Convert slocum binary data (*.ebd/*.dbd) to raw netcdf files.


   :Parameters:

       **indir** : str
           Directory with the raw ``*.ebd`` (science) and ``*.dbd`` (flight) files.
           These usually come from ``card_offload/Science/SENTLOGS`` or
           ``card_offload/Science/LOGS``, and ``card_offload/Main_board/SENTLOGS``
           and ``card_offload/Main_board/LOGS`. Recommend ``binary``

       **outdir** : str
           Directory to write the matching ``*.ebd.nc`` and ``*.dbd.nc`` files.
           Recommend ``rawnc``.

       **cacdir** : str
           Directory where the cached CAC sensor lists are kept.  These
           lists are often in directories like ``../Main_board/STATE/CACHE/``
           and ``../Science/STATE/CACHE/``, and the files in these directories
           should be copied to this directory by the user.  Recommend ``cac``

       **sensorlist** : str
           Text file with sensor list for this glider.  This filters the many
           sensors on the slocum gliders to just the ones listed here.  The file
           is text, comments deelineated as ``# a comment`` and a new entry
           on each line.

       **deploymentyaml** : str
           YAML text file with deployment information for this glider.

       **incremental** : bool, optional
           If *True* (default), only netcdf files that are older than the
           binary files are re-parsed.



   :Returns:

       **status** : bool
           *True* success.








   .. rubric:: Notes

   This process can be slow for many files.



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.. py:function:: merge_rawnc(indir, outdir, deploymentyaml, scisuffix='EBD', glidersuffix='DBD')

   
   Merge all the raw netcdf files in indir.  These are meant to be
   the raw flight and science files from the slocum.


   :Parameters:

       **indir** : str
           Directory where the raw ``*.ebd.nc`` and ``*.dbd.nc`` files are.
           Recommend: ``./rawnc``

       **outdir** : str
           Directory where merged raw netcdf files will be put. Recommend:
           ``./rawnc/``.  Note that the netcdf files will be named following
           the data in *deploymentyaml*:
           ``glider_nameglider_serial-YYYYmmddTHHMM-rawebd.nc`` and
           ``...rawdbd.nc``.

       **deploymentyaml** : str
           YAML text file with deployment information for this glider.














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.. py:function:: raw_to_timeseries(indir, outdir, deploymentyaml, *, profile_filt_time=100, profile_min_time=300)

   



   :Parameters:

       **indir** : string
           Directory with raw netcdf files.

       **outdir** : string
           Directory to put the merged timeseries files.

       **profile_filt_time** : float
           time in seconds over which to smooth the pressure time series for
           finding up and down profiles (note, doesn't filter the data that is
           saved)

       **profile_min_time** : float
           minimum time to consider a profile an actual profile (seconds)

       **Returns**
           ..

       **-------**
           ..

       **outname** : string
           name of the new merged netcdf file.














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.. py:function:: parse_gliderState(fname)

   
   Parse time, lat, and lon from a gliderstate file


   :Parameters:

       **fname** : string or Path
           Location of the gliderState.xml file for the glider



   :Returns:

       **dat** : xarray
           xarray with fields time, lon, lat











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.. py:function:: parse_logfiles(files)

   
   Parse time, lat, lon, and amph_total from glider logfiles.


   :Parameters:

       **files** : list of strings or Paths
           List of logfiles to parse.  Should be sorted.



   :Returns:

       **out** : xarray
           xarray data set with fields time, lon, lat, ampH indexed by surfacing.
           More could be added.











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