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

    Click :ref:`here <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.





.. image:: /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
    from scipy import ndimage
    import matplotlib.pyplot as plt

    np.random.seed(1)
    n = 10
    l = 256
    im = np.zeros((l, l))
    points = l*np.random.random((2, n**2))
    im[(points[0]).astype(np.int), (points[1]).astype(np.int)] = 1
    im = ndimage.gaussian_filter(im, sigma=l/(4.*n))

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


    img = mask + 0.3*np.random.randn(*mask.shape)

    binary_img = img > 0.5

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

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

    l = 128

    plt.subplot(141)
    plt.imshow(binary_img[:l, :l], cmap=plt.cm.gray)
    plt.axis('off')
    plt.subplot(142)
    plt.imshow(open_img[:l, :l], cmap=plt.cm.gray)
    plt.axis('off')
    plt.subplot(143)
    plt.imshow(close_img[:l, :l], cmap=plt.cm.gray)
    plt.axis('off')
    plt.subplot(144)
    plt.imshow(mask[:l, :l], cmap=plt.cm.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()


**Total running time of the script:** ( 0 minutes  0.056 seconds)


.. _sphx_glr_download_advanced_image_processing_auto_examples_plot_clean_morpho.py:


.. only :: html

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



  .. container:: sphx-glr-download

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



  .. container:: sphx-glr-download

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


.. only:: html

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

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