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author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-02-16 14:58:11 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-02-16 14:58:11 +0000 |
commit | 518acce63202c7b89fa3f76467e50eee7630cf62 (patch) | |
tree | d9877e63720c6a6fa2cef113182fe1178c049cb1 /src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py | |
parent | df173dbefd275c54d8f5e33794d51709b887d2d3 (diff) |
Remove pandas examples and use of OFF files interfaces to be more consistent (pandas interface is not that hard to be done)
Add of distance matrix in Rips
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2081 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 3a3b24f0824eed2710edb5bf17d120039973bf62
Diffstat (limited to 'src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py')
-rwxr-xr-x | src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py | 71 |
1 files changed, 71 insertions, 0 deletions
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py new file mode 100755 index 00000000..2b726f90 --- /dev/null +++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -0,0 +1,71 @@ +#!/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='RipsComplex creation from ' + 'a distance matrix read in a OFF file.', + epilog='Example: ' + 'example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py ' + '-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3' + '- Constructs a Rips complex with the ' + 'points from the given OFF file.') +parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument("-e", "--max_edge_length", type=float, default=0.5) +parser.add_argument("-d", "--max_dimension", type=int, default=1) +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("RipsComplex creation from distance matrix read in a csv file") + + message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) + print(message) + + rips_complex = gudhi.RipsComplex(off_file=args.file, max_edge_length=args.max_edge_length) + simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_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: + gudhi.diagram_persistence(diag) + else: + print(args.file, "is not a valid OFF file") + + f.close() |