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

.. only:: html

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

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

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

.. _sphx_glr_examples_strain_mapping_strain_mapping.py:


Strain Mapping
==============

Strain mapping in pyxem is done by fitting a :class:`~.signals.tensor_field.DisplacementGradientMap` to the data.
This can be thought of as image distortion around some central point.

.. GENERATED FROM PYTHON SOURCE LINES 8-13

.. code-block:: Python


    from pyxem.data import simulated_strain
    import hyperspy.api as hs









.. GENERATED FROM PYTHON SOURCE LINES 14-18

In this example we will create a simulated strain map using the :meth:`~.data.simulated_strain` function.
This just creates a simulated diffraction pattern and applies a simple "strain" to it. In this
case using simulated data is slightly easier for demonstration purposes. If you want to use
real data the :meth:`~.data.zrnb_precipitate` dataset is a good example of strain from a precipitate.

.. GENERATED FROM PYTHON SOURCE LINES 18-28

.. code-block:: Python


    strained_signal = simulated_strain(
        navigation_shape=(32, 32),
        signal_shape=(512, 512),
        disk_radius=20,
        num_electrons=1e5,
        strain_matrix=None,
        lazy=True,
    )








.. GENERATED FROM PYTHON SOURCE LINES 29-31

The first thing we want to do is to find peaks within the diffraction pattern. I'd recommend
using the :meth:`~.signals.diffraction2d.get_diffraction_vectors` method

.. GENERATED FROM PYTHON SOURCE LINES 31-37

.. code-block:: Python


    strained_signal.calibration.center = (
        None  # First set the center to be (256, 256) or the center of the signal
    )
    template_matched = strained_signal.template_match_disk(disk_r=20, subtract_min=False)
    template_matched.plot(vmin=0.4)



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


    *

      .. image-sg:: /examples/strain_mapping/images/sphx_glr_strain_mapping_001.png
         :alt: strain mapping
         :srcset: /examples/strain_mapping/images/sphx_glr_strain_mapping_001.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /examples/strain_mapping/images/sphx_glr_strain_mapping_002.png
         :alt:  Signal
         :srcset: /examples/strain_mapping/images/sphx_glr_strain_mapping_002.png
         :class: sphx-glr-multi-img


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Plotting the template matched signal and setting ``vmin`` is a good way to see what threshold you
should use for the :meth:`~.signals.diffraction2d.get_diffraction_vectors` method.

.. GENERATED FROM PYTHON SOURCE LINES 40-49

.. code-block:: Python


    diffraction_vectors = template_matched.get_diffraction_vectors(
        threshold_abs=0.4, min_distance=5
    )

    markers = diffraction_vectors.to_markers(color="w", sizes=5, alpha=0.5)
    strained_signal.plot()
    strained_signal.add_marker(markers)




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


    *

      .. image-sg:: /examples/strain_mapping/images/sphx_glr_strain_mapping_003.png
         :alt: strain mapping
         :srcset: /examples/strain_mapping/images/sphx_glr_strain_mapping_003.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /examples/strain_mapping/images/sphx_glr_strain_mapping_004.png
         :alt:  Signal
         :srcset: /examples/strain_mapping/images/sphx_glr_strain_mapping_004.png
         :class: sphx-glr-multi-img


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Determining the Strain
----------------------
We can just use the first ring of the diffraction pattern to determine the strain. We can do this by
using the :meth:`~.signals.DiffractionVectors.filter_magnitude` method. You can also look at the
:ref:`filtering vectors <_sphx_glr_examples_vectors_masking_vectors.py>` example to see
how to select which vectors you want to use more generally. You can also just manually input the un-strained
vectors or use simulated/ rotated vectors as well.

.. GENERATED FROM PYTHON SOURCE LINES 57-70

.. code-block:: Python


    first_ring_vectors = diffraction_vectors.filter_magnitude(
        min_magnitude=0.1,
        max_magnitude=1,
    )
    unstrained_vectors = first_ring_vectors.inav[0, 0]

    strain_maps = first_ring_vectors.get_strain_maps(
        unstrained_vectors=unstrained_vectors, return_residuals=False
    )

    strain_maps.plot()




.. image-sg:: /examples/strain_mapping/images/sphx_glr_strain_mapping_005.png
   :alt: e11, e22, e12, theta
   :srcset: /examples/strain_mapping/images/sphx_glr_strain_mapping_005.png
   :class: sphx-glr-single-img


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    [<Axes: title={'center': 'e11'}, xlabel='x axis (nm)', ylabel='y axis (nm)'>, <Axes: title={'center': 'e22'}, xlabel='x axis (nm)', ylabel='y axis (nm)'>, <Axes: title={'center': 'e12'}, xlabel='x axis (nm)', ylabel='y axis (nm)'>, <Axes: title={'center': 'theta'}, xlabel='x axis (nm)', ylabel='y axis (nm)'>]



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Some final notes about strain mapping. In general, you want to use as many pixels as possible. 512 x 512 is a good
place to start.  You can do strain mapping with fewer pixels, but the results will be less accurate. Precession
also helps improve the results as does having a thinner sample both of which reduce the effects of dynamical
diffraction.

.. GENERATED FROM PYTHON SOURCE LINES 77-78

sphinx_gallery_thumbnail_number = 5


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

   **Total running time of the script:** (0 minutes 31.719 seconds)


.. _sphx_glr_download_examples_strain_mapping_strain_mapping.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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