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

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_auto_examples_segmentation_plot_random_walker_segmentation.py>`
        to download the full example code or to run this example in your browser via Binder

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

.. _sphx_glr_auto_examples_segmentation_plot_random_walker_segmentation.py:


==========================
Random walker segmentation
==========================

The random walker algorithm [1]_  determines the segmentation of an image from
a set of markers labeling several phases (2 or more). An anisotropic diffusion
equation is solved with tracers initiated at the markers' position. The local
diffusivity coefficient is greater if neighboring pixels have similar values,
so that diffusion is difficult across high gradients. The label of each unknown
pixel is attributed to the label of the known marker that has the highest
probability to be reached first during this diffusion process.

In this example, two phases are clearly visible, but the data are too
noisy to perform the segmentation from the histogram only. We determine
markers of the two phases from the extreme tails of the histogram of gray
values, and use the random walker for the segmentation.

.. [1] *Random walks for image segmentation*, Leo Grady, IEEE Trans. Pattern
       Anal. Mach. Intell. 2006 Nov; 28(11):1768-83 :DOI:`10.1109/TPAMI.2006.233`

.. GENERATED FROM PYTHON SOURCE LINES 23-63



.. image-sg:: /auto_examples/segmentation/images/sphx_glr_plot_random_walker_segmentation_001.png
   :alt: Noisy data, Markers, Segmentation
   :srcset: /auto_examples/segmentation/images/sphx_glr_plot_random_walker_segmentation_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    import numpy as np
    import matplotlib.pyplot as plt

    from skimage.segmentation import random_walker
    from skimage.data import binary_blobs
    from skimage.exposure import rescale_intensity
    import skimage

    rng = np.random.default_rng()

    # Generate noisy synthetic data
    data = skimage.img_as_float(binary_blobs(length=128, rng=1))
    sigma = 0.35
    data += rng.normal(loc=0, scale=sigma, size=data.shape)
    data = rescale_intensity(data, in_range=(-sigma, 1 + sigma), out_range=(-1, 1))

    # The range of the binary image spans over (-1, 1).
    # We choose the hottest and the coldest pixels as markers.
    markers = np.zeros(data.shape, dtype=np.uint)
    markers[data < -0.95] = 1
    markers[data > 0.95] = 2

    # Run random walker algorithm
    labels = random_walker(data, markers, beta=10, mode='bf')

    # Plot results
    fig, (ax1, ax2, ax3) = plt.subplots(1, 3, figsize=(8, 3.2), sharex=True, sharey=True)
    ax1.imshow(data, cmap='gray')
    ax1.axis('off')
    ax1.set_title('Noisy data')
    ax2.imshow(markers, cmap='magma')
    ax2.axis('off')
    ax2.set_title('Markers')
    ax3.imshow(labels, cmap='gray')
    ax3.axis('off')
    ax3.set_title('Segmentation')

    fig.tight_layout()
    plt.show()


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

   **Total running time of the script:** (0 minutes 0.424 seconds)


.. _sphx_glr_download_auto_examples_segmentation_plot_random_walker_segmentation.py:

.. only:: html

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

    .. container:: binder-badge

      .. image:: images/binder_badge_logo.svg
        :target: https://mybinder.org/v2/gh/scikit-image/scikit-image/v0.23.2?filepath=notebooks/auto_examples/segmentation/plot_random_walker_segmentation.ipynb
        :alt: Launch binder
        :width: 150 px

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

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

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

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


.. only:: html

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

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