:orphan:

.. To get rid of WARNING: document isn't included in any toctree

Persistence graphical tools user manual
=======================================
Definition
----------
.. include:: persistence_graphical_tools_sum.inc


Show persistence as a barcode
-----------------------------

.. note::
    this function requires matplotlib and numpy to be available

This function can display the persistence result as a barcode:

.. plot::
   :include-source:

    import matplotlib.pyplot as plot
    import gudhi

    off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off'
    point_cloud = gudhi.read_points_from_off_file(off_file=off_file)

    rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.7)
    simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
    diag = simplex_tree.persistence(min_persistence=0.4)

    gudhi.plot_persistence_barcode(diag)
    plot.show()

Show persistence as a diagram
-----------------------------

.. note::
    this function requires matplotlib and numpy to be available

This function can display the persistence result as a diagram:

.. plot::
   :include-source:

    import matplotlib.pyplot as plot
    import gudhi

    # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method
    persistence_file=gudhi.__root_source_dir__ + \
        '/data/persistence_diagram/rips_on_tore3D_1307.pers'
    gudhi.plot_persistence_diagram(persistence_file=persistence_file,
        legend=True)
    plot.show()

Persistence density
-------------------

.. note::
    this function requires matplotlib, numpy and scipy to be available

If you want more information on a specific dimension, for instance:

.. plot::
   :include-source:

    import matplotlib.pyplot as plot
    import gudhi
    # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method
    persistence_file=gudhi.__root_source_dir__ + \
        '/data/persistence_diagram/rips_on_tore3D_1307.pers'
    birth_death = gudhi.read_persistence_intervals_in_dimension(
        persistence_file=persistence_file,
        only_this_dim=1)
    pers_diag = [(1, elt) for elt in birth_death]
    # Use subplots to display diagram and density side by side
    fig, axes = plot.subplots(nrows=1, ncols=2, figsize=(12, 5))
    gudhi.plot_persistence_diagram(persistence=pers_diag,
        axes=axes[0])
    gudhi.plot_persistence_density(persistence=pers_diag,
        dimension=1, legend=True, axes=axes[1])
    plot.show()