.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/segmentation/plot_rag_merge.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_rag_merge.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_rag_merge.py:


====================================
Region adjacency graph (RAG) Merging
====================================

This example constructs a Region Adjacency Graph (RAG) and progressively merges
regions that are similar in color. Merging two adjacent regions produces
a new region with all the pixels from the merged regions. Regions are merged
until no highly similar region pairs remain.

.. GENERATED FROM PYTHON SOURCE LINES 12-81



.. image-sg:: /auto_examples/segmentation/images/sphx_glr_plot_rag_merge_001.png
   :alt: plot rag merge
   :srcset: /auto_examples/segmentation/images/sphx_glr_plot_rag_merge_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    from skimage import data, io, segmentation, color
    from skimage import graph
    import numpy as np


    def _weight_mean_color(graph, src, dst, n):
        """Callback to handle merging nodes by recomputing mean color.

        The method expects that the mean color of `dst` is already computed.

        Parameters
        ----------
        graph : RAG
            The graph under consideration.
        src, dst : int
            The vertices in `graph` to be merged.
        n : int
            A neighbor of `src` or `dst` or both.

        Returns
        -------
        data : dict
            A dictionary with the `"weight"` attribute set as the absolute
            difference of the mean color between node `dst` and `n`.
        """

        diff = graph.nodes[dst]['mean color'] - graph.nodes[n]['mean color']
        diff = np.linalg.norm(diff)
        return {'weight': diff}


    def merge_mean_color(graph, src, dst):
        """Callback called before merging two nodes of a mean color distance graph.

        This method computes the mean color of `dst`.

        Parameters
        ----------
        graph : RAG
            The graph under consideration.
        src, dst : int
            The vertices in `graph` to be merged.
        """
        graph.nodes[dst]['total color'] += graph.nodes[src]['total color']
        graph.nodes[dst]['pixel count'] += graph.nodes[src]['pixel count']
        graph.nodes[dst]['mean color'] = (
            graph.nodes[dst]['total color'] / graph.nodes[dst]['pixel count']
        )


    img = data.coffee()
    labels = segmentation.slic(img, compactness=30, n_segments=400, start_label=1)
    g = graph.rag_mean_color(img, labels)

    labels2 = graph.merge_hierarchical(
        labels,
        g,
        thresh=35,
        rag_copy=False,
        in_place_merge=True,
        merge_func=merge_mean_color,
        weight_func=_weight_mean_color,
    )

    out = color.label2rgb(labels2, img, kind='avg', bg_label=0)
    out = segmentation.mark_boundaries(out, labels2, (0, 0, 0))
    io.imshow(out)
    io.show()


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

   **Total running time of the script:** (0 minutes 1.610 seconds)


.. _sphx_glr_download_auto_examples_segmentation_plot_rag_merge.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_rag_merge.ipynb
        :alt: Launch binder
        :width: 150 px

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

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

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

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


.. only:: html

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

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