plesty.fss.line_fit
===================

.. py:module:: plesty.fss.line_fit

.. autoapi-nested-parse::

   Finding and fitting the lines of one spectrum, for :class:`plesty.fss.tracking.LineTracker`.

   Both steps are the analysis's own: lines are found with
   :meth:`~plesty.lib.data.SpectrumData.find_peaks` and fitted with
   :class:`~plesty.lib.analyzer.SpectrumFit`, so a line the tracker follows during
   a sweep is found and fitted as the analysis does after it.



Functions
---------

.. autoapisummary::

   plesty.fss.line_fit.saved_fit
   plesty.fss.line_fit.check_fit_options
   plesty.fss.line_fit.find_lines
   plesty.fss.line_fit.fit_line_positions


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

.. py:function:: saved_fit(path: Any) -> Any

   Load the line fit an analysis saved, given the path of its document.

   Here rather than beside the tracker because this module is where a line
   fit is produced, and a fit read back is the same thing arriving another
   way — the tracker itself reaches for nothing outside this package.

   :param path: The document's path.

   :returns: The analyzer's ``fit`` output.

   :raises Exception: Whatever reading it raises — a document still being
       written, or one from a version that saved a different shape.


.. py:function:: check_fit_options(fit_options: Mapping[str, Any]) -> None

   Refuse fit options :class:`~plesty.lib.analyzer.SpectrumFit` would refuse.

   :raises ValueError: If an option is invalid.


.. py:function:: find_lines(wavelength: numpy.ndarray, reference: numpy.ndarray, prominence: Optional[float], distance: int) -> numpy.ndarray

   Return the positions of the lines in *reference*, shortest wavelength first.

   :param wavelength: The axis, in nm.
   :param reference: The spectrum to search, e.g. the median of the spectra so far.
   :param prominence: Minimum height of a line above its surroundings, in counts.
   :param distance: Minimum separation of two lines, in pixels.


.. py:function:: fit_line_positions(wavelength: numpy.ndarray, counts: numpy.ndarray, seeds: numpy.ndarray, fit_options: Mapping[str, Any]) -> numpy.ndarray

   Fit the lines of one spectrum, starting from *seeds*, and return their positions.

   Fit-quality warnings are not raised: one spectrum at a time says little, and
   the analysis reports them for the whole sweep.

   :param wavelength: The axis, in nm.
   :param counts: The spectrum.
   :param seeds: Starting position of each line, in nm.
   :param fit_options: :class:`~plesty.lib.analyzer.SpectrumFit` options other than ``peaks``.

   :returns: The fitted position of each line, ``nan`` for all when the fit fails.

   :raises ImportError: If the fitting extra is not installed. A spectrum that
       cannot be fitted is ordinary and becomes ``nan``; an environment
       that cannot fit *anything* is not, and swallowing it means every
       line of every spectrum silently reads as unfittable — a viewer
       drawing no markers at all, with nothing to say why.