.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/processing/centering_the_zero_beam.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_examples_processing_centering_the_zero_beam.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_examples_processing_centering_the_zero_beam.py:


Centering the Zero Beam
=======================

.. GENERATED FROM PYTHON SOURCE LINES 7-8

Making a Dummy Dataset with a Zero Beam that systematically deviates from the center

.. GENERATED FROM PYTHON SOURCE LINES 8-19

.. code-block:: Python

    import hyperspy.api as hs
    import pyxem as pxm

    s = pxm.data.tilt_boundary_data(correct_pivot_point=False)

    # Getting the Position of the Zero beam
    # -------------------------------------
    # The zero beam position can be obtained using the :meth:`get_direct_beam_position` method.

    shifts = s.get_direct_beam_position(method="blur", sigma=5, half_square_width=20)
    hs.plot.plot_images(shifts.T)  # Plotting the shifts



.. image-sg:: /examples/processing/images/sphx_glr_centering_the_zero_beam_001.png
   :alt:  (0,),  (1,)
   :srcset: /examples/processing/images/sphx_glr_centering_the_zero_beam_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    [                                        ] | 0% Completed | 139.81 us
    [                                        ] | 0% Completed | 100.45 ms
    [########################################] | 100% Completed | 200.82 ms

    [                                        ] | 0% Completed | 131.71 us
    [########################################] | 100% Completed | 100.42 ms

    [<Axes: title={'center': ' (0,)'}>, <Axes: title={'center': ' (1,)'}>]



.. GENERATED FROM PYTHON SOURCE LINES 20-42

.. code-block:: Python


    # Making a Linear Plane
    # ---------------------
    # In many instances the zero beam position will vary systematically with the scan position.
    # This can be corrected by fitting a linear plane to the zero beam position using the
    # :meth:`make_linear_plane` method.
    shifts.make_linear_plane()  # Making a linear plane to remove the systematic shift
    hs.plot.plot_images(shifts.T)  # Plotting the shifts after making a linear plane

    # Centering the Zero Beam
    # -----------------------
    # The zero beam can be centered using the :meth:`center_direct_beam` method.

    centered = s.center_direct_beam(shifts=shifts, inplace=False)
    pacbed_centered = (
        centered.sum()
    )  # Plotting the sum of the dataset to check that the zero beam is centered
    pacbed = (
        s.sum()
    )  # Plotting the sum of the dataset to check that the zero beam is centered

    hs.plot.plot_images([pacbed, pacbed_centered], label=["Original", "Centered"])



.. rst-class:: sphx-glr-horizontal


    *

      .. image-sg:: /examples/processing/images/sphx_glr_centering_the_zero_beam_002.png
         :alt:  (0,),  (1,)
         :srcset: /examples/processing/images/sphx_glr_centering_the_zero_beam_002.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /examples/processing/images/sphx_glr_centering_the_zero_beam_003.png
         :alt: Original, Centered
         :srcset: /examples/processing/images/sphx_glr_centering_the_zero_beam_003.png
         :class: sphx-glr-multi-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    [                                        ] | 0% Completed | 163.25 us
    [                                        ] | 0% Completed | 100.46 ms
    [########################################] | 100% Completed | 200.80 ms

    [<Axes: title={'center': 'Original'}>, <Axes: title={'center': 'Centered'}>]




.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 2.379 seconds)


.. _sphx_glr_download_examples_processing_centering_the_zero_beam.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: centering_the_zero_beam.ipynb <centering_the_zero_beam.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: centering_the_zero_beam.py <centering_the_zero_beam.py>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_