pyextal.dinfo
=============

.. py:module:: pyextal.dinfo


Classes
-------

.. autoapisummary::

   pyextal.dinfo.BaseDiffractionInfo
   pyextal.dinfo.CBEDDiffractionInfo
   pyextal.dinfo.LARBEDDiffractionInfo


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

.. py:class:: BaseDiffractionInfo

   Base class for storing diffraction information and refined results.

   .. attribute:: dp

      The diffraction pattern as a NumPy array of np.float32.

      :type: np.ndarray

   .. attribute:: thickness

      Thickness of the sample in Angstroms.

      :type: float

   .. attribute:: tiltX

      Tilt angle around the x-axis in degrees.

      :type: float

   .. attribute:: tiltY

      Tilt angle around the y-axis in degrees.

      :type: float

   .. attribute:: gl

      X-axis length in experimental diffraction pattern space.

      :type: float

   .. attribute:: datpath

      Path to the .dat file containing crystal information.

      :type: str


   .. py:attribute:: dp
      :type:  numpy.ndarray[numpy.float32]


   .. py:attribute:: thickness
      :type:  float


   .. py:attribute:: tiltX
      :type:  float


   .. py:attribute:: tiltY
      :type:  float


   .. py:attribute:: gl
      :type:  float


   .. py:attribute:: datpath
      :type:  str


   .. py:method:: __post_init__()

      Initializes additional attributes after the dataclass is created.



   .. py:property:: includeBeam

      Gets the list of Miller indices for beams included in the simulation.


   .. py:method:: updateSF(beam: tuple, value: numpy.ndarray[numpy.float32])

      Updates the structure factor for a given beam and its symmetric equivalents.

      :param beam: The Miller index (h, k, l) of the beam to update.
      :type beam: tuple
      :param value: A 4-element NumPy array containing the new structure
                    factor values.
      :type value: np.ndarray

      :raises ValueError: If the provided `value` is not a 4-element NumPy array.



   .. py:method:: getSF(beam: tuple) -> numpy.ndarray

      Retrieves the structure factor for a given beam.

      If the beam is part of a symmetry group, the group's structure factor is
      returned. Otherwise, it looks up the Independent Atom Model (IAM) value.

      :param beam: The Miller index (h, k, l) of the beam.
      :type beam: tuple

      :returns: The structure factor of the beam.
      :rtype: np.ndarray



   .. py:method:: getAllSF() -> tuple[numpy.ndarray, numpy.ndarray]

      Retrieves all unique structure factors and their corresponding beams.

      :returns:

                A tuple containing:
                    - An array of all unique structure factors.
                    - An array of one representative beam (h, k, l) for each factor.
      :rtype: tuple[np.ndarray, np.ndarray]



   .. py:method:: save(path: str | pathlib.Path)

      Saves the diffraction information to a file.

      Note: This method is not yet implemented.

      :param path: The path to the file where the data will be saved.
      :type path: str | Path



   .. py:method:: save_hkl(path: str | pathlib.Path, glen: float = 5.0, minOutput: float = 0.001) -> None

      Saves structure factors to a .hkl file for VESTA Fourier synthesis.

      :param path: Path to the output .hkl file.
      :type path: str | Path
      :param glen: Maximum length of the g-vector to include,
                   in inverse Angstroms. Defaults to 5.0.
      :type glen: float, optional
      :param minOutput: The minimum IAM structure factor magnitude
                        to be included in the output file. Defaults to 1e-3.
      :type minOutput: float, optional



.. py:class:: CBEDDiffractionInfo

   Bases: :py:obj:`BaseDiffractionInfo`


   Stores and processes Convergent Beam Electron Diffraction (CBED) data.

   This class extends `BaseDiffractionInfo` with attributes and methods specific
   to CBED experiments, including detector parameters and background correction.

   .. attribute:: dtpar

      Detector DQE parameters [varB, delta, A, g, m].

      :type: list[float]

   .. attribute:: mtf

      The Modulation Transfer Function as a NumPy array.

      :type: np.ndarray

   .. attribute:: background

      Background level of the diffraction pattern.

      :type: float

   .. attribute:: numIter

      Number of iterations for Lucy-Richardson
      deconvolution. Defaults to 25.

      :type: int, optional


   .. py:attribute:: dtpar
      :type:  list[float]


   .. py:attribute:: mtf
      :type:  numpy.ndarray[numpy.float32]


   .. py:attribute:: background
      :type:  float


   .. py:attribute:: numIter
      :type:  int
      :value: 25



.. py:class:: LARBEDDiffractionInfo

   Bases: :py:obj:`BaseDiffractionInfo`


   Stores and processes Large Angle Rocking Beam Electron Diffraction (LARBED) data.

   This class extends `BaseDiffractionInfo` with attributes specific to LARBED
   experiments, such as g-vector indices and variance maps.

   .. attribute:: gindex

      An array of g-vector indices.

      :type: np.ndarray

   .. attribute:: varianceMaps

      Variance maps associated with the
      diffraction pattern. If not provided, it defaults to a copy of the
      diffraction pattern.

      :type: np.ndarray, optional


   .. py:attribute:: gindex
      :type:  numpy.ndarray


   .. py:attribute:: varianceMaps
      :type:  numpy.ndarray[numpy.float32]
      :value: None



   .. py:method:: __post_init__()

      Initializes variance maps if they are not provided.