Glossary
--------

.. glossary::


    Acquisition
        Acquisition refers to recording and timestamping ADCP and
        Navigation feeds.  For modern ADCP data it is done with either UHDAS or VmDAS.
        (Prior to the development of UHDAS, DAS 2.48 was used for the original narrowband 150kHz instrument.)
        Time stamping always comes from the acquisition computer.  For UHDAS, that
        time is always in UTC and is synced to an  NTP server (if available on the ship).
        For VmDAS data, times are usually UTC, and there is no control over the time zone.

    ADCP Data
        NMEA serial feeds/line/data coming from RDI ADCPs

    CODAS Averages
        :term:`ADCP data` and :term:`Navigation data` that went through :term:`Preliminary Processing`.

    CODAS Processing
        :ref:`CODAS Processing  <uhdas_codas_processing_flowchart>`
        refers to turning acquired data into scientific products.
        It is composed of two distinct stages: preliminary and post processing.
        :term:`Preliminary processing` occurs once, to stage the data.
        :term:`Post-processing` may
        involve some repetition (eg. editing or calibration).

    Config Directory
        The config directory contains cruise-specific files defining parameters required
        throughout the UHDAS Data processing.   For VmDAS data, the config directlry also
        contains information needed to convert the VmDAS data into UHDAS-style data.
        By convention, the cruise-specfic configuration file used for processing has the suffix
        ``*_proc.py``.

    Control File
        The control file resides in the processing directory, and is a sonar-specific file
        defining parameters
        required for use in the single-ping processing or for reformatting pre-averaged data
        into CODAS averages. By convention, its file name
        is ``qpy.cnt``.

    Data Products
        Data products are generated by removing ship speed from measured velocities,
        possibly averaging further, and outputting data products in other forms.
        Data formats supported include html, netCDF, matlab files, and figures.

    Navigation Data
        NMEA serial feeds/line/data with position (GPS) or heading

    Preliminary Processing
        Depending on the input data, the preliminary processing:
        - converts VmDAS single-ping Data into UHDAS-style Data
        - applies Single-ping Processing to UHDAS and UHDAS-style Data
        - formats VmDAS Data and UHDAS Single-Ping Data into CODAS Averages
        Note that the different steps of the preliminary processing stated above
        are automatically managed by :ref:`adcp_database_maker.py <adcp_database_maker_intro>`.
        or manually managed via a combination of :ref:`comand-lines actions <commandline_intro>` .

    Project Directory
        The Project directory is defined
        as the user's main location for processing a given cruise.
        It is useful to use the cruise name in the name.  This directory
        can be created within the work flow of :ref:`adcp_database_maker.py <adcp_database_maker_intro>`

    Processing Directory
        Also referred as "Sonar Processing Directory" or "ADCP Processing Diretory", this folder contains
        the CODAS averages of a given sonar. This directory is usually created
        via :ref:`adcp_database_maker.py <adcp_database_maker_intro>`        and, ultimately, adcptree.py.

    Post-Processing
        the post-processing is composed of:

        - Manual Editing (using :ref:`patch_hcorr.py <patch_hcorr>`
          and :ref:`dataviewer.py <dataviewer-index>`)
        - Calibration (using :ref:`quick_adcp.py <quickadcp_overview>`)
        - Generating Products (:ref:`quick_adcp.py <quickadcp_overview>`,
          :ref:`quick_web.py <quick_web>`,
          and :ref:`adcp_nc.py<extract_netcdf>` (with :ref:`output described here <read_netcdf>`)

    Single-Ping processing
        The single-ping processing is a key component of the preliminary processing
        of VmDas or UHDAS  single-ping level data.  Single-ping processing includes
        transformations (from beam to earth coordinates), editing out acoustic interference,
        editing out data below the bottom (including the side-lobe interference),
        additional single-ping editing, and  averaging in time.
        Read this `article <https://journals.ametsoc.org/doi/pdf/10.1175/1520-0426(2003)020%3C0872%3AADCOTR%3E2.0.CO%3B2>`_
        for more details on the single-ping processing.

    Sonar
        Sonar is the combination of an ADCP instrument type (2 letters), a sampling frequency
        and a ping-type. Ex.: os75nb, os38bb. Some ADCPs don't have variable ping-type
        thus their related sonar name is simply their instrument type and frequency.
        Ex.: wh300, bb150


    UHDAS Data
      ADCP and Navigation Data Acquired at sea by UHDAS
      (see `folder architecture </../UHDAS_OPERATIONS/UHDAS_atsea/cruisedir_contents.html>`_).
      It is composed of UHDAS single-ping Data and Codas Averages

    UHDAS-style Data
        ADCP and navigation data, in the directory structure and naming convention of
        UHDASdata, produced by the conversion of VmDAS Single-ping Data
        using either :ref:`adcp_database_maker.py <adcp_database_maker_intro>`
        or a combination of :ref:`command-line actions <commandline_intro>` .

    UHDAS single-ping Data
       Single-ping level ADCP and Navigation data acquired by UHDAS, i.e. not averaged. It is composed
       of the following folders: ``raw``, ``rbin`` and ``gbin`` (add link to folder architecture diagram)


    VmDAS Data
        ADCP and Navigation Data Acquired at sea by VmDAS.
        It is composed of VmDAS Single-ping Data ( ``ENR``,  ``N1R``, ``N2R`` (``N3R``).
        and VmDAS Averages ( ``LTA`` and ``STA``).

    VmDAS Single-ping Data
        Single-ping level ADCP and Navigatation data acquired by VmDAS
        It is composed of the following file types:  ``ENR``,  ``N1R``, ``N2R`` (``N3R``).

    VmDAS Averages
        ADCP and Navigation data that were averaged over time by VmDAS.
        into short-term and long-ter averages.
        They are contained in the following file types:   ``LTA`` and ``STA``.

    \*.proc.txt
        Automated reformatting of VmDAS LTA or STA data includes the creation of a
        post-processing guide with hints about the next steps.  The post-processing
        guide is stored in the Projext directory and typically has a suffix ``*proc.txt``.

    \*.info.txt
        Automated preliminary processing of any VmDAS data includes the discovery of
        information about the VmDAS dataset, such as ping types, averaging length,
        and transducer offset (EA command).  This information is stored in the Projext directory
        with a suffix ``*info.txt``.  The same file can be created by running ``vmdas_info.py``.