.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/example_watershed.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_example_watershed.py>`
        to download the full example code.

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

.. _sphx_glr_auto_examples_example_watershed.py:


.. _example_watershed:

===================================
Example of watershed in slam
===================================

.. GENERATED FROM PYTHON SOURCE LINES 8-16

.. code-block:: Python


    # Authors:
    # Lucile Hashimoto lucile-hashimoto
    # Guillaume Auzias <guillaume.auzias@univ-amu.fr>

    # License: MIT
    # sphinx_gallery_thumbnail_number = 2








.. GENERATED FROM PYTHON SOURCE LINES 17-21

NOTE: there is no visualization tool in slam, but we provide at the
 end of this script exemplare code to do the visualization with
 an external solution
##############################################################################

.. GENERATED FROM PYTHON SOURCE LINES 23-24

importation of slam modules

.. GENERATED FROM PYTHON SOURCE LINES 24-28

.. code-block:: Python

    import slam.io as sio
    import slam.watershed as swat
    import slam.sulcal_graph as ssg








.. GENERATED FROM PYTHON SOURCE LINES 29-30

loading an examplar mesh and corresponding texture

.. GENERATED FROM PYTHON SOURCE LINES 30-37

.. code-block:: Python

    path_to_mesh = "../examples/data/example_mesh.gii"
    path_to_mask = None
    path_to_output = ""

    mesh = sio.load_mesh(path_to_mesh)
    side = "left"








.. GENERATED FROM PYTHON SOURCE LINES 38-39

compute curvature, dpf and voronoi

.. GENERATED FROM PYTHON SOURCE LINES 39-41

.. code-block:: Python

    _, dpf, voronoi = swat.compute_mesh_features(mesh, save=False, outdir=path_to_output, check_if_exist=True)








.. GENERATED FROM PYTHON SOURCE LINES 42-43

normalize watershed thresholds

.. GENERATED FROM PYTHON SOURCE LINES 43-46

.. code-block:: Python

    thresh_dist, thresh_ridge, thresh_area = swat.normalize_thresholds(voronoi, thresh_dist=20.0, thresh_ridge=1.5,
                                                                       thresh_area=50.0, side=side)





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

 .. code-block:: none


            Computing the surface area





.. GENERATED FROM PYTHON SOURCE LINES 47-48

define the exclusion mask (cingular pole)

.. GENERATED FROM PYTHON SOURCE LINES 48-53

.. code-block:: Python

    if path_to_mask is not None:
        mask = sio.load_texture(path_to_mask).darray[0]
    else:
        mask = None








.. GENERATED FROM PYTHON SOURCE LINES 54-55

extract sulcal pits and associated basins

.. GENERATED FROM PYTHON SOURCE LINES 55-57

.. code-block:: Python

    basins, ridges, adjacency = swat.watershed(mesh, voronoi, dpf, thresh_dist, thresh_ridge, thresh_area, mask)





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

 .. code-block:: none

    Computing watershed by flooding...
    Distance between 2 pits: 5.3 mm - Ridge height: 1.5 mm
    Number of basins found: 27
    nb of basins to remove: 0




.. GENERATED FROM PYTHON SOURCE LINES 58-59

generate the textures from watershed outputs

.. GENERATED FROM PYTHON SOURCE LINES 59-61

.. code-block:: Python

    tex_labels, tex_pits, tex_ridges = swat.get_textures_from_dict(mesh, basins, ridges, save=True, outdir=path_to_output)








.. GENERATED FROM PYTHON SOURCE LINES 62-63

generate the sulcal graph

.. GENERATED FROM PYTHON SOURCE LINES 63-65

.. code-block:: Python

    g = ssg.get_sulcal_graph(adjacency, basins, ridges, save=True, outdir=path_to_output)





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

 .. code-block:: none

    Graph saved in graph.gpickle




.. GENERATED FROM PYTHON SOURCE LINES 66-67

generate the textures from graph

.. GENERATED FROM PYTHON SOURCE LINES 67-67

.. code-block:: Python

    tex_labels, tex_pits, tex_ridges = ssg.get_textures_from_graph(g, mesh, save=True, outdir=path_to_output)







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

   **Total running time of the script:** (0 minutes 2.761 seconds)


.. _sphx_glr_download_auto_examples_example_watershed.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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