diff options
Diffstat (limited to 'src/cython/example')
5 files changed, 93 insertions, 8 deletions
diff --git a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py index ab5fc1e9..386f8457 100755 --- a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py +++ b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py @@ -45,13 +45,14 @@ 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'): + point_cloud = gudhi.read_off(off_file=args.file) print("#####################################################################") print("RipsComplex creation from points read in a OFF file") message = "RipsComplex with max_edge_length=" + repr(args.threshold) print(message) - rips_complex = gudhi.RipsComplex(off_file=args.file, + rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=args.threshold) rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension) @@ -67,7 +68,7 @@ with open(args.file, 'r') as f: message = "AlphaComplex with max_edge_length=" + repr(args.threshold) print(message) - alpha_complex = gudhi.AlphaComplex(off_file=args.file) + alpha_complex = gudhi.AlphaComplex(points=point_cloud) alpha_stree = alpha_complex.create_simplex_tree(max_alpha_square=(args.threshold * args.threshold)) message = "Number of simplices=" + repr(alpha_stree.num_simplices()) diff --git a/src/cython/example/bottleneck_basic_example.py b/src/cython/example/bottleneck_basic_example.py index 31cecb29..a7fa01c1 100755 --- a/src/cython/example/bottleneck_basic_example.py +++ b/src/cython/example/bottleneck_basic_example.py @@ -28,8 +28,6 @@ __author__ = "Francois Godi, Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 INRIA" __license__ = "GPL v3" -import gudhi - diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]] diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]] 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 new file mode 100755 index 00000000..aa82ef71 --- /dev/null +++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -0,0 +1,84 @@ +#!/usr/bin/env python + +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. + + Author(s): Vincent Rouvreau + + 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/>. +""" + +__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.') +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_boot", 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() + +if not (-1. < args.min_edge_correlation < 1.): + print("Wrong value of the treshold corelation (should be between -1 and 1).") + sys.exit(1) + +print("#####################################################################") +print("Caution: as persistence diagrams points will be under the diagonal,") +print("bottleneck distance and persistence graphical tool will not work") +print("properly, this is a known issue.") + +print("#####################################################################") +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) +# 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) +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()) + +# 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))] + +if args.no_diagram == False: + pplot = gudhi.plot_persistence_diagram(invert_diag, band_boot=args.band_boot) + pplot.show() 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 index 3baebd17..c8aac240 100755 --- 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 @@ -30,12 +30,12 @@ __copyright__ = "Copyright (C) 2016 INRIA" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='RipsComplex creation from ' - 'a distance matrix read in a OFF file.', + 'a distance matrix read in a csv 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.') + 'distance matrix from the given csv 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) @@ -50,7 +50,8 @@ 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(csv_file=args.file, max_edge_length=args.max_edge_length) +distance_matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file=args.file) +rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, 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()) diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py index 5951eedf..544b68c9 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -53,7 +53,8 @@ with open(args.file, 'r') as f: 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) + point_cloud = gudhi.read_off(off_file=args.file) + rips_complex = gudhi.RipsComplex(points=point_cloud, 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()) |