pyextal.larbed.calibration
==========================

.. py:module:: pyextal.larbed.calibration

.. autoapi-nested-parse::

   Detector MTF calibration from a probe / vacuum scan.

   .. note::

      Legacy. Because :meth:`pyextal.larbed.LARBEDAnalysis.IntegrateLarbed`
      integrates over an aperture, deconvolving against the MTF mainly adds noise
      and is normally skipped. The step-length measurement here is still useful on
      its own for calibrating the tilt scan.



Classes
-------

.. autoapisummary::

   pyextal.larbed.calibration.LARBEDCalibration


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

.. py:class:: LARBEDCalibration(file_name)

   Measures the detector point-spread function and the tilt-scan step length.

   The input is a reference scan taken with no sample and descan off, so only
   the direct beam is present and it walks across the detector. The usual
   sequence is :meth:`load_data`, :meth:`find_peaks`,
   :meth:`calculate_average_step_length`, :meth:`crop_peaks`,
   :meth:`interpolate`, and :meth:`calculate_mtf`.

   :ivar data: The 4D reference stack.
   :vartype data: np.ndarray
   :ivar peaks: Fitted (x, y) beam position at each scan step.
   :vartype peaks: np.ndarray
   :ivar average_step_length: Mean beam displacement per scan step, in
                              detector pixels.
   :vartype average_step_length: float
   :ivar probe_image: The interpolated probe shape.
   :vartype probe_image: np.ndarray
   :ivar mtf_2d: The modulation transfer function, in the Fourier
                 domain.

   :vartype mtf_2d: np.ndarray


   .. py:attribute:: file_name


   .. py:attribute:: data
      :value: []



   .. py:attribute:: crop_data
      :value: []



   .. py:attribute:: probe_image
      :value: None



   .. py:attribute:: mtf_2d
      :value: None



   .. py:attribute:: peaks
      :value: None



   .. py:attribute:: roi_size
      :value: None



   .. py:method:: load_data(type=0)

      Reads the reference scan and displays its middle pattern.

      :param type: Detector layout, passed to
                   :func:`pyextal.larbed.empad.ReadRaw`. Defaults to 0.
      :type type: int, optional



   .. py:method:: meanimage()

      Averages the reference stack.

      :returns: The mean 2D pattern.
      :rtype: np.ndarray



   .. py:method:: find_peaks(start=1, end=255)

      Fits the beam position in every pattern of a square scan sub-region.

      :param start: First scan index of the sub-region. Defaults to 1.
      :type start: int, optional
      :param end: One past the last scan index. Defaults to 255.
      :type end: int, optional



   .. py:method:: crop_peaks(crop_size=20)

      Crops and sub-pixel aligns a patch around each fitted beam position.

      :param crop_size: Side length of each patch in pixels.
                        Defaults to 20.
      :type crop_size: int, optional



   .. py:method:: calculate_average_step_length()

      Measures the mean beam displacement per scan step, in detector pixels.

      This is the quantity that converts the tilt scan into reciprocal space;
      combined with the detector calibration and the length of the x-axis
      reflection it gives the ``gl`` passed to the refinement stage.



   .. py:method:: interpolate()

      Rescales the averaged probe patch by the measured step length.



   .. py:method:: calculate_mtf(pad_size=256)

      Transforms the probe image into a normalised Fourier-domain MTF.

      The result is suitable for :func:`pyextal.LucyRichardson.lucy_Richardson`
      with ``mode='fourier'``.

      :param pad_size: Size the probe image is zero-padded to
                       before the transform. Defaults to 256.
      :type pad_size: int, optional