diff options
Diffstat (limited to 'src/cython/doc/persistence_graphical_tools_user.rst')
| -rw-r--r-- | src/cython/doc/persistence_graphical_tools_user.rst | 37 |
1 files changed, 24 insertions, 13 deletions
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst index 292915eb..b2124fdd 100644 --- a/src/cython/doc/persistence_graphical_tools_user.rst +++ b/src/cython/doc/persistence_graphical_tools_user.rst @@ -12,6 +12,9 @@ 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:: @@ -19,16 +22,22 @@ This function can display the persistence result as a barcode: import gudhi - perseus_file = gudhi.__root_source_dir__ + '/data/bitmap/3d_torus.txt' - periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=perseus_file) - diag = periodic_cc.persistence() - print("diag = ", diag) - plt = gudhi.plot_persistence_barcode(diag) - plt.show() + off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off' + point_cloud = gudhi.read_off(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() 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:: @@ -43,6 +52,12 @@ This function can display the persistence result as a diagram: legend=True) plt.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:: @@ -50,13 +65,9 @@ If you want more information on a specific dimension, for instance: 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' - diag = \ - gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file=\ - persistence_file) - dim = 1 - # Display all points with some transparency - plt = gudhi.plot_persistence_diagram([(dim,interval) for interval in diag[dim]], - max_plots=0, alpha=0.1) + plt = gudhi.plot_persistence_density(persistence_file=persistence_file, + max_intervals=0, dimension=1, legend=True) plt.show() |