diff options
Diffstat (limited to 'src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py')
-rwxr-xr-x | src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py | 75 |
1 files changed, 39 insertions, 36 deletions
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index 0c9dfc43..3571580b 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -4,48 +4,42 @@ import gudhi import sys 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. +""" 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 - Author(s): Vincent Rouvreau + Copyright (C) 2017 Inria - Copyright (C) 2017 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/>. + Modification(s): + - YYYY/MM Author: Description of the modification """ __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2017 Inria" -__license__ = "GPL v3" - -parser = argparse.ArgumentParser(description='RipsComplex creation from ' - 'a correlation matrix read in a csv file.', - epilog='Example: ' - 'example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py ' - '-f ../data/correlation_matrix/lower_triangular_correlation_matrix.csv -e 12.0 -d 3' - '- Constructs a Rips complex with the ' - 'correlation matrix from the given csv file.') +__license__ = "MIT" + +parser = argparse.ArgumentParser( + description="RipsComplex creation from " "a correlation matrix read in a csv file.", + epilog="Example: " + "example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py " + "-f ../data/correlation_matrix/lower_triangular_correlation_matrix.csv -e 12.0 -d 3" + "- Constructs a Rips complex with the " + "correlation matrix from the given csv file.", +) parser.add_argument("-f", "--file", type=str, required=True) parser.add_argument("-c", "--min_edge_correlation", type=float, default=0.5) parser.add_argument("-d", "--max_dimension", type=int, default=1) -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') +parser.add_argument("-b", "--band", type=float, default=0.0) +parser.add_argument( + "--no-diagram", + default=False, + action="store_true", + help="Flag for not to display the diagrams", +) args = parser.parse_args() -if not (-1. < args.min_edge_correlation < 1.): +if not (-1.0 < args.min_edge_correlation < 1.0): print("Wrong value of the treshold corelation (should be between -1 and 1).") sys.exit(1) @@ -60,12 +54,18 @@ print("RipsComplex creation from correlation matrix read in a csv file") message = "RipsComplex with min_edge_correlation=" + repr(args.min_edge_correlation) print(message) -correlation_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file) +correlation_matrix = gudhi.read_lower_triangular_matrix_from_csv_file( + csv_file=args.file +) # Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get a distance matrix: -distance_matrix = [[1.-correlation_matrix[i][j] for j in range(len(correlation_matrix[i]))] for i in range(len(correlation_matrix))] - -rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, - max_edge_length=1.-args.min_edge_correlation) +distance_matrix = [ + [1.0 - correlation_matrix[i][j] for j in range(len(correlation_matrix[i]))] + for i in range(len(correlation_matrix)) +] + +rips_complex = gudhi.RipsComplex( + distance_matrix=distance_matrix, max_edge_length=1.0 - args.min_edge_correlation +) simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) message = "Number of simplices=" + repr(simplex_tree.num_simplices()) @@ -77,7 +77,10 @@ print("betti_numbers()=") print(simplex_tree.betti_numbers()) # invert the persistence diagram -invert_diag = [(diag[pers][0],(1.-diag[pers][1][0], 1.-diag[pers][1][1])) for pers in range(len(diag))] +invert_diag = [ + (diag[pers][0], (1.0 - diag[pers][1][0], 1.0 - diag[pers][1][1])) + for pers in range(len(diag)) +] if args.no_diagram == False: pplot = gudhi.plot_persistence_diagram(invert_diag, band=args.band) |