diff options
Diffstat (limited to 'src/cython/example')
-rwxr-xr-x | src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py | 71 | ||||
-rwxr-xr-x | src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py (renamed from src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py) | 64 |
2 files changed, 104 insertions, 31 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() diff --git a/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py index 8af1b767..eb1c4ed5 100755 --- a/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import gudhi -import pandas import argparse """This file is part of the Gudhi Library. The Gudhi library @@ -30,40 +29,43 @@ __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.', + 'points read in a OFF 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') + 'example/rips_complex_diagram_persistence_from_off_file_example.py ' + '-f ../data/points/tore3D_300.off -a 0.6' + '- 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("-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() -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_edge_length=args.max_edge_length) - -simplex_tree = rips_complex.create_simplex_tree(max_dimension=len(points.values[0])) - -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) +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 points read in a OFF 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() |