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

.. only:: html

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

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

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

.. _sphx_glr_advanced_image_processing_auto_examples_plot_clean_morpho.py:


Cleaning segmentation with mathematical morphology
===================================================

An example showing how to clean segmentation with mathematical
morphology: removing small regions and holes.

.. GENERATED FROM PYTHON SOURCE LINES 9-55



.. image-sg:: /advanced/image_processing/auto_examples/images/sphx_glr_plot_clean_morpho_001.png
   :alt: plot clean morpho
   :srcset: /advanced/image_processing/auto_examples/images/sphx_glr_plot_clean_morpho_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    import numpy as np
    import scipy as sp
    import matplotlib.pyplot as plt

    rng = np.random.default_rng(27446968)
    n = 10
    l = 256
    im = np.zeros((l, l))
    points = l * rng.random((2, n**2))
    im[(points[0]).astype(int), (points[1]).astype(int)] = 1
    im = sp.ndimage.gaussian_filter(im, sigma=l / (4.0 * n))

    mask = (im > im.mean()).astype(float)


    img = mask + 0.3 * rng.normal(size=mask.shape)

    binary_img = img > 0.5

    # Remove small white regions
    open_img = sp.ndimage.binary_opening(binary_img)
    # Remove small black hole
    close_img = sp.ndimage.binary_closing(open_img)

    plt.figure(figsize=(12, 3))

    l = 128

    plt.subplot(141)
    plt.imshow(binary_img[:l, :l], cmap="gray")
    plt.axis("off")
    plt.subplot(142)
    plt.imshow(open_img[:l, :l], cmap="gray")
    plt.axis("off")
    plt.subplot(143)
    plt.imshow(close_img[:l, :l], cmap="gray")
    plt.axis("off")
    plt.subplot(144)
    plt.imshow(mask[:l, :l], cmap="gray")
    plt.contour(close_img[:l, :l], [0.5], linewidths=2, colors="r")
    plt.axis("off")

    plt.subplots_adjust(wspace=0.02, hspace=0.3, top=1, bottom=0.1, left=0, right=1)

    plt.show()


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

   **Total running time of the script:** (0 minutes 0.075 seconds)


.. _sphx_glr_download_advanced_image_processing_auto_examples_plot_clean_morpho.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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