r2r_ctd.derived
===============

.. py:module:: r2r_ctd.derived

.. autoapi-nested-parse::

   Functions that take some existing data, and either extract from or transform it

   e.g. the :py:func:`get_longitude` function tries to extract the longitude information from the hdr file



Attributes
----------

.. autoapisummary::

   r2r_ctd.derived.logger


Functions
---------

.. autoapisummary::

   r2r_ctd.derived._parse_coord
   r2r_ctd.derived.get_longitude
   r2r_ctd.derived.get_latitude
   r2r_ctd.derived._normalize_date_strings
   r2r_ctd.derived.get_time
   r2r_ctd.derived.make_con_report
   r2r_ctd.derived.get_model
   r2r_ctd.derived._con_report_extract_sensors
   r2r_ctd.derived.get_con_report_sn
   r2r_ctd.derived.get_hdr_sn
   r2r_ctd.derived.make_derive_psa
   r2r_ctd.derived.make_binavg_psa
   r2r_ctd.derived.make_datcnv_psa
   r2r_ctd.derived.make_cnvs


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

.. py:data:: logger

.. py:function:: _parse_coord(coord: str) -> float | None

   Parses a spaced separated DDM coordinate with hemisphere to decimal degrees

   >>> _parse_coord("32 52.02 N")
   32.867
   >>> _parse_coord("117 15.435 W")
   -117.25725


.. py:function:: get_longitude(ds: xarray.Dataset) -> float | None

   Get the cast longitude from NMEA header

   .. admonition:: WHOI Divergence
       :class: warning

       The original code from WHOI tries to also get this from the ``** Longitude`` line
       but I think the ``**`` means it is a comment and can be *anything* the user puts in.


.. py:function:: get_latitude(ds: xarray.Dataset) -> float | None

   Get the cast latitude from NMEA header

   .. admonition:: WHOI Divergence
       :class: warning

       The original code from WHOI tries to also get this from the ``** Latitude`` line
       but I think the ``**`` means it is a comment and can be *anything* the user puts in.


.. py:function:: _normalize_date_strings(date: str) -> str

   Try to make the date strings in sbe hdr files have a consistent format

   There can be variable whitespace between time elements, this function
   tries to remove them so we can use the normal strptime method.

   >>> _normalize_date_strings("Oct 09 2019  17:05:53")
   'Oct 09 2019 17:05:53'


.. py:function:: get_time(ds: xarray.Dataset) -> datetime.datetime | None

   Gets the time from the hdr file

   In the following priority order:
   * NMEA UTC (Time)
   * System UTC
   * System Upload Time


.. py:function:: make_con_report(ds: xarray.Dataset)

   Runs ConReport.exe on the xmlcon file in the dataset


.. py:function:: get_model(con_report: str) -> str | None

   Given a configuration report, get the SBE model string

   Uses string matching and doesn't parse/transform the model lines in the config report.


.. py:function:: _con_report_extract_sensors(con_report: str) -> list[str]

   Extract a list of sensors from a configuration report, adds some virtual sensors if NMEA information was added to the data

   This is looking for lines in the form of::

       1) channel type, sensor name

   eg::

       1) Frequency 0, Temperature

   Then extracting the "sensor name" part of that line.

   If "NMEA position data added" is "yes", virtual latitude and longitude sensors are added to the list.
   If "NMEA time added" is "yes", a virtual "ETime" sensor is added to the list.
   If the model of the instrument is an SBE911, a "pump" sensor is added to the list.


.. py:function:: get_con_report_sn(con_report: str, instrument: str) -> set[str]

   Get the serial numbers for instruments from the configuration report (XMLCON).


.. py:function:: get_hdr_sn(hdr: str, instrument: str) -> str | None

   Get an instruments serial number from the .hdr file.

   That this serial number intersects with the set generated by :py:func:`get_con_report_sn` is reported in the QA.


.. py:function:: make_derive_psa(con_report: str) -> bytes

   Makes the derive psa config file for derive.exe based on the configuration report, will add second density calculation if dual channel


.. py:function:: make_binavg_psa(con_report: str) -> bytes

   Get the binage psa config from :py:func:`r2r_ctd.sbe.binavg_template` and return it unmodified.


.. py:function:: make_datcnv_psa(con_report: str) -> bytes

   Make the datcnv psa config based on the configuration report, populating the CalcArray element


.. py:function:: make_cnvs(ds: xarray.Dataset) -> dict[str, xarray.Dataset]

   Makes the derived cnv files

   Creates all the various configuration files, then passes everything off to the companion container to actually be processed.