.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/processing/background_subtraction.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_background_subtraction.py>`
        to download the full example code.

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

.. _sphx_glr_examples_processing_background_subtraction.py:


Background subtraction
======================

If your diffraction data is noisy, you might want to subtract the background from the
dataset. Pyxem offers some built-in functionality for this, with the
`subtract_diffraction_background` class method. Custom filtering is also possible, an
example is shown in the 'Filtering Data'-example.

.. GENERATED FROM PYTHON SOURCE LINES 10-35

.. code-block:: Python


    import pyxem as pxm
    import hyperspy.api as hs

    s = pxm.data.tilt_boundary_data()

    s_filtered = s.subtract_diffraction_background(
        "difference of gaussians",
        inplace=False,
        min_sigma=3,
        max_sigma=20,
    )

    s_filtered_h = s.subtract_diffraction_background("h-dome", inplace=False, h=0.7)


    hs.plot.plot_images(
        [s.inav[2, 2], s_filtered.inav[2, 2], s_filtered_h.inav[2, 2]],
        label=["Original", "Difference of Gaussians", "H-Dome"],
        tight_layout=True,
        norm="symlog",
        cmap="viridis",
        colorbar=None,
    )




.. image-sg:: /examples/processing/images/sphx_glr_background_subtraction_001.png
   :alt: Original, Difference of Gaussians, H-Dome
   :srcset: /examples/processing/images/sphx_glr_background_subtraction_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none


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      regional_filter(frame / max_value, **kwargs), footprint=square(3)
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      output = function(test_data, **kwargs)

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      regional_filter(frame / max_value, **kwargs), footprint=square(3)
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    [<Axes: title={'center': 'Original'}, xlabel='kx axis (px)', ylabel='ky axis (px)'>, <Axes: title={'center': 'Difference of Gaussians'}, xlabel='kx axis (px)', ylabel='ky axis (px)'>, <Axes: title={'center': 'H-Dome'}, xlabel='kx axis (px)', ylabel='ky axis (px)'>]



.. GENERATED FROM PYTHON SOURCE LINES 36-44

======================
Filtering Polar Images
======================
The available methods differ for `Diffraction2D` datasets and `PolarDiffraction2D`
datasets.

Set the center of the diffraction pattern to its default,
i.e. the middle of the image

.. GENERATED FROM PYTHON SOURCE LINES 44-47

.. code-block:: Python


    s.calibration.center = None








.. GENERATED FROM PYTHON SOURCE LINES 48-49

Transform to polar coordinates

.. GENERATED FROM PYTHON SOURCE LINES 49-72

.. code-block:: Python


    s_polar = s.get_azimuthal_integral2d(npt=100, mean=True)

    s_polar_filtered = s_polar.subtract_diffraction_background(
        "radial median",
        inplace=False,
    )

    s_polar_filtered2 = s_polar.subtract_diffraction_background(
        "radial percentile",
        percentile=70,
        inplace=False,
    )

    hs.plot.plot_images(
        [s_polar.inav[2, 2], s_polar_filtered.inav[2, 2], s_polar_filtered2.inav[2, 2]],
        label=["Original (polar)", "Radial Median", "Radial Percentile"],
        tight_layout=True,
        norm="symlog",
        cmap="viridis",
        colorbar=None,
    )




.. image-sg:: /examples/processing/images/sphx_glr_background_subtraction_002.png
   :alt: Original (polar), Radial Median, Radial Percentile
   :srcset: /examples/processing/images/sphx_glr_background_subtraction_002.png
   :class: sphx-glr-single-img


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

 .. code-block:: none


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    [<Axes: title={'center': 'Original (polar)'}, xlabel='Radians axis (Rad)', ylabel='Radius axis (px)'>, <Axes: title={'center': 'Radial Median'}, xlabel='Radians axis (Rad)', ylabel='Radius axis (px)'>, <Axes: title={'center': 'Radial Percentile'}, xlabel='Radians axis (Rad)', ylabel='Radius axis (px)'>]




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

   **Total running time of the script:** (0 minutes 11.650 seconds)


.. _sphx_glr_download_examples_processing_background_subtraction.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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