.. 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 ` 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 [ ] | 0% Completed | 178.12 us [ ] | 0% Completed | 109.71 ms [ ] | 0% Completed | 210.07 ms [ ] | 0% Completed | 310.43 ms [ ] | 0% Completed | 410.77 ms [ ] | 0% Completed | 511.07 ms [ ] | 0% Completed | 611.37 ms [ ] | 0% Completed | 711.66 ms [ ] | 0% Completed | 811.95 ms [ ] | 0% Completed | 912.24 ms [ ] | 0% Completed | 1.01 s [ ] | 0% Completed | 1.11 s [ ] | 0% Completed | 1.21 s [ ] | 0% Completed | 1.31 s [ ] | 0% Completed | 1.41 s [ ] | 0% Completed | 1.51 s [ ] | 0% Completed | 1.61 s [ ] | 0% Completed | 1.71 s [ ] | 0% Completed | 1.81 s [########################################] | 100% Completed | 1.92 s /home/docs/checkouts/readthedocs.org/user_builds/pyxem/envs/v0.19.0/lib/python3.10/site-packages/hyperspy/misc/utils.py:1437: UserWarning: Possible precision loss converting image of type float32 to uint8 as required by rank filters. 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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 [ ] | 0% Completed | 191.46 us [ ] | 0% Completed | 107.02 ms [ ] | 0% Completed | 207.36 ms [ ] | 0% Completed | 307.67 ms [ ] | 0% Completed | 407.97 ms [ ] | 0% Completed | 508.28 ms [ ] | 0% Completed | 608.57 ms [ ] | 0% Completed | 708.87 ms [ ] | 0% Completed | 814.10 ms [ ] | 0% Completed | 919.33 ms [ ] | 0% Completed | 1.02 s [########################################] | 100% Completed | 1.12 s [ ] | 0% Completed | 158.75 us [ ] | 0% Completed | 106.93 ms [ ] | 0% Completed | 207.31 ms [########################################] | 100% Completed | 307.71 ms [ ] | 0% Completed | 157.39 us [ ] | 0% Completed | 113.89 ms [ ] | 0% Completed | 214.20 ms [ ] | 0% Completed | 314.68 ms [ ] | 0% Completed | 415.01 ms [ ] | 0% Completed | 515.38 ms [ ] | 0% Completed | 615.74 ms [ ] | 0% Completed | 716.13 ms [ ] | 0% Completed | 816.50 ms [ ] | 0% Completed | 916.82 ms [ ] | 0% Completed | 1.02 s [ ] | 0% Completed | 1.12 s [ ] | 0% Completed | 1.22 s [ ] | 0% Completed | 1.32 s [ ] | 0% Completed | 1.42 s [ ] | 0% Completed | 1.52 s [ ] | 0% Completed | 1.62 s [ ] | 0% Completed | 1.72 s [ ] | 0% Completed | 1.82 s [ ] | 0% Completed | 1.92 s [########################################] | 100% Completed | 2.02 s [, , ] .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 30.379 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 ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: background_subtraction.py ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_