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#!/usr/bin/env python
import gudhi
import matplotlib.pyplot as plt
import time
""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
Author(s): Vincent Rouvreau
Copyright (C) 2016 Inria
Modification(s):
- YYYY/MM Author: Description of the modification
"""
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2020 Inria"
__license__ = "MIT"
print("#####################################################################")
print("RipsComplex (only the one-skeleton) creation from tore3D_300.off file")
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=12.0)
simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
print('1. Rips complex is of dimension ', simplex_tree.dimension(), ' - ',
simplex_tree.num_simplices(), ' simplices - ',
simplex_tree.num_vertices(), ' vertices.')
# Expansion of this one-skeleton would require a lot of memory. Let's collapse it
start = time.process_time()
simplex_tree.collapse_edges()
print('2. Rips complex is of dimension ', simplex_tree.dimension(), ' - ',
simplex_tree.num_simplices(), ' simplices - ',
simplex_tree.num_vertices(), ' vertices.')
simplex_tree.expansion(3)
diag = simplex_tree.persistence()
print("Collapse, expansion and persistence computation took ", time.process_time() - start, " sec.")
# 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(diag, axes=axes[0])
axes[0].set_title("Persistence after 1 collapse")
# Collapse can be performed several times. Let's collapse it 3 times
start = time.process_time()
simplex_tree.collapse_edges(nb_iterations = 3)
print('3. Rips complex is of dimension ', simplex_tree.dimension(), ' - ',
simplex_tree.num_simplices(), ' simplices - ',
simplex_tree.num_vertices(), ' vertices.')
simplex_tree.expansion(3)
diag = simplex_tree.persistence()
print("Collapse, expansion and persistence computation took ", time.process_time() - start, " sec.")
gudhi.plot_persistence_diagram(diag, axes=axes[1])
axes[1].set_title("Persistence after 3 more collapses")
# Plot the 2 persistence diagrams side to side to check the persistence is the same
plt.show()
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