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

.. only:: html

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

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

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

.. _sphx_glr_auto_examples_plot_tilt_series.py:


Tilting real crystals
=====================

Every grain is a crystal with a full 3D orientation (orix), and diffraction comes from
diffsims structure factors. Tilting the stage moves grains through Bragg conditions: the
Laue circle of a silicon lamella sweeps across its pattern, and gold grains in a thin film
switch between dark and bright in bright-field images.

.. GENERATED FROM PYTHON SOURCE LINES 10-40



.. image-sg:: /auto_examples/images/sphx_glr_plot_tilt_series_001.png
   :alt: alpha -2 deg, alpha -1 deg, alpha +0 deg, alpha +1 deg, alpha +2 deg
   :srcset: /auto_examples/images/sphx_glr_plot_tilt_series_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    import matplotlib.pyplot as plt
    import numpy as np

    from de_twin import DigitalTwin, ManualClock
    from de_twin.state import Projection

    lamella = DigitalTwin("PN junction lamella", camera="DESim", clock=ManualClock(), seed=3)
    lamella.column.set("Magnification", 4000)
    lamella.column.set_projection(Projection.DIFFRACTION)

    film = DigitalTwin("Au thin film 20 nm", camera="DESim", clock=ManualClock(), seed=3)
    film.column.set("Magnification", 30000)
    film.column.set_intensity(0.75)

    tilts = [-2.0, -1.0, 0.0, 1.0, 2.0]
    fig, axes = plt.subplots(2, len(tilts), figsize=(12, 5.2))
    for i, a in enumerate(tilts):
        lamella.column.move_stage(alpha=a)
        dp = np.sqrt(lamella.flux(lamella.request()))
        axes[0, i].imshow(dp, cmap="gray", vmax=np.percentile(dp, 99.97))
        axes[0, i].set_title(f"alpha {a:+.0f} deg", fontsize=9)
        film.column.move_stage(alpha=a)
        axes[1, i].imshow(film.flux(film.request()), cmap="gray")
    for ax in axes.ravel():
        ax.axis("off")
    fig.text(0.01, 0.74, "Si lamella\ndiffraction", va="center", fontsize=9)
    fig.text(0.01, 0.26, "Au film\nbright field", va="center", fontsize=9)
    fig.tight_layout(rect=(0.06, 0, 1, 1))
    plt.show()


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

   **Total running time of the script:** (0 minutes 3.690 seconds)


.. _sphx_glr_download_auto_examples_plot_tilt_series.py:

.. only:: html

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

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

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

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

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

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_tilt_series.zip <plot_tilt_series.zip>`


.. only:: html

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

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