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Diffstat (limited to 'src/python/doc/persistence_graphical_tools_user.rst')
| -rw-r--r-- | src/python/doc/persistence_graphical_tools_user.rst | 60 |
1 files changed, 45 insertions, 15 deletions
diff --git a/src/python/doc/persistence_graphical_tools_user.rst b/src/python/doc/persistence_graphical_tools_user.rst index b2124fdd..e1d28c71 100644 --- a/src/python/doc/persistence_graphical_tools_user.rst +++ b/src/python/doc/persistence_graphical_tools_user.rst @@ -12,62 +12,92 @@ Definition 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 plt import gudhi off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off' - point_cloud = gudhi.read_off(off_file=off_file) + 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) - plot = gudhi.plot_persistence_barcode(diag) - plot.show() + gudhi.plot_persistence_barcode(diag) + plt.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 plt 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' - plt = gudhi.plot_persistence_diagram(persistence_file=persistence_file, + ax = gudhi.plot_persistence_diagram(persistence_file=persistence_file, legend=True) + # We can modify the title, aspect, etc. + ax.set_title("Persistence diagram of a torus") + ax.set_aspect("equal") # forces to be square shaped + plt.show() + +Note that (as barcode and density) it can also take a simple `np.array` +of shape (N x 2) encoding a persistence diagram (in a given dimension). + +.. plot:: + :include-source: + + import matplotlib.pyplot as plt + import gudhi + import numpy as np + d = np.array([[0., 1.], [1., 2.], [1., np.inf]]) + gudhi.plot_persistence_diagram(d) plt.show() Persistence density ------------------- -.. note:: - this function requires matplotlib, numpy and scipy to be available +:Requires: `SciPy <installation.html#scipy>`_ If you want more information on a specific dimension, for instance: .. plot:: :include-source: + import matplotlib.pyplot as plt 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' - plt = gudhi.plot_persistence_density(persistence_file=persistence_file, - max_intervals=0, dimension=1, legend=True) + 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 = plt.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]) plt.show() + +LaTeX support +------------- + +If you are facing issues with `LaTeX <installation.html#latex>`_ rendering, you can still deactivate LaTeX rendering by +saying: + +.. code-block:: python + + import gudhi + gudhi.persistence_graphical_tools._gudhi_matplotlib_use_tex=False |