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#!/usr/bin/env python
import gudhi
import argparse
"""This file is part of the Gudhi Library. The Gudhi library
(Geometric Understanding in Higher Dimensions) is a generic C++
library for computational topology.
Author(s): Vincent Rouvreau
Copyright (C) 2016 Inria
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
__author__ = "Vincent Rouvreau"
__copyright__ = "Copyright (C) 2016 Inria"
__license__ = "GPL v3"
parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from '
'points read in a OFF file.',
epilog='Example: '
'example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py '
'-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2'
'- Constructs a weak witness complex with the '
'points from the given OFF file.')
parser.add_argument("-f", "--file", type=str, required=True)
parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
parser.add_argument("-d", "--limit_dimension", type=int, required=True)
parser.add_argument("-b", "--band", type=float, default=0.)
parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
args = parser.parse_args()
with open(args.file, 'r') as f:
first_line = f.readline()
if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
print("#####################################################################")
print("EuclideanWitnessComplex creation from points read in a OFF file")
witnesses = gudhi.read_off(off_file=args.file)
landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks)
message = "EuclideanWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \
" - Number of landmarks=" + repr(args.number_of_landmarks)
print(message)
witness_complex = gudhi.EuclideanWitnessComplex(witnesses=witnesses, landmarks=landmarks)
simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square,
limit_dimension=args.limit_dimension)
message = "Number of simplices=" + repr(simplex_tree.num_simplices())
print(message)
diag = simplex_tree.persistence()
print("betti_numbers()=")
print(simplex_tree.betti_numbers())
if args.no_diagram == False:
pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
pplot.show()
else:
print(args.file, "is not a valid OFF file")
f.close()
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