diff options
Diffstat (limited to 'src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py')
-rwxr-xr-x | src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py | 68 |
1 files changed, 68 insertions, 0 deletions
diff --git a/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py b/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py new file mode 100755 index 00000000..bcf2fbcb --- /dev/null +++ b/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py @@ -0,0 +1,68 @@ +#!/usr/bin/env python + +import gudhi +import pandas +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" + +print("#####################################################################") +print("RipsComplex creation from points read in a file") + +parser = argparse.ArgumentParser(description='RipsComplex creation from ' + 'points read in a file.', + epilog='Example: ' + 'example/rips_complex_diagram_persistence_with_pandas_interface_example.py ' + '../data/2000_random_points_on_3D_Torus.csv ' + '- Constructs a rips complex with the ' + 'points from the given file. File format ' + 'is X1, X2, ..., Xn') +parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument("-e", "--max-edge-length", type=float, default=0.5) +parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') + +args = parser.parse_args() + +points = pandas.read_csv(args.file, header=None) + +message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) +print(message) + +rips_complex = gudhi.RipsComplex(points=points.values, + max_dimension=len(points.values[0]), max_edge_length=args.max_edge_length) + +message = "Number of simplices=" + repr(rips_complex.num_simplices()) +print(message) + +rips_complex.initialize_filtration() +diag = rips_complex.persistence() + +print("betti_numbers()=") +print(rips_complex.betti_numbers()) + +if args.no_diagram == False: + gudhi.diagram_persistence(diag) |