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

.. only:: html

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

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

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

.. _sphx_glr_generated_gallery_contours_boundary_chan_vese.py:


=====================================
Adding Chan-Vese Contours to an Image
=====================================

This example shows how to add a contour based on the chan-vese segmentation of the image.

The Chan-vese algorithm is a level set method for image segmentation.
It is based on the Mumford-Shah functional and is designed to segment images without edges.

In this example, we will the `ripplemapper.analyse` module to segment the image and add the resulting contour to the image.

The CV segmentation is a more unreliable way to form the contours.

.. GENERATED FROM PYTHON SOURCE LINES 17-18

We can load an image into a RippleImage object using the RippleImage class and then run `add_chan_vese_contours` to add Chan-Vese contours to the image.

.. GENERATED FROM PYTHON SOURCE LINES 18-28

.. code-block:: Python


    import matplotlib.pyplot as plt

    from ripplemapper.analyse import add_chan_vese_contours
    from ripplemapper.classes import RippleImage
    from ripplemapper.data.example import example_data

    ripple_img = RippleImage(example_data[2])
    add_chan_vese_contours(ripple_img)








.. GENERATED FROM PYTHON SOURCE LINES 29-30

Plotting the image and its contours

.. GENERATED FROM PYTHON SOURCE LINES 30-34

.. code-block:: Python


    ripple_img.plot(include_contours=True)
    plt.show()




.. image-sg:: /generated/gallery/contours/images/sphx_glr_boundary_chan_vese_001.png
   :alt: RippleImage: 1_00375_sample.tif
   :srcset: /generated/gallery/contours/images/sphx_glr_boundary_chan_vese_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 35-37

We can also add the Chan-Vese contours to a image where we use a combination of the divergence of the image and the regular image.
This might improve the segmentation technique

.. GENERATED FROM PYTHON SOURCE LINES 37-41

.. code-block:: Python


    add_chan_vese_contours(ripple_img, use_gradients=True, overwrite=True)
    ripple_img.plot(include_contours=True)
    plt.show()



.. image-sg:: /generated/gallery/contours/images/sphx_glr_boundary_chan_vese_002.png
   :alt: RippleImage: 1_00375_sample.tif
   :srcset: /generated/gallery/contours/images/sphx_glr_boundary_chan_vese_002.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /home/docs/checkouts/readthedocs.org/user_builds/ripplemapper/envs/latest/lib/python3.12/site-packages/ripplemapper/analyse.py:151: UserWarning: Overwriting Chan-Vese contour for image: /home/docs/checkouts/readthedocs.org/user_builds/ripplemapper/envs/latest/lib/python3.12/site-packages/ripplemapper/data/example/1_00375_sample.tif
      warnings.warn(f"Overwriting Chan-Vese contour for image: {ripple_image.source_file}")





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

   **Total running time of the script:** (0 minutes 1.568 seconds)


.. _sphx_glr_download_generated_gallery_contours_boundary_chan_vese.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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