From 3787c1b1473a590515a62bfb0b616ce17045f731 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 5 Feb 2018 10:02:52 +0000 Subject: Do like C++ example git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@3217 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: cc963c77e30c649e7428afc609bac4ba1f515a37 --- ...rsistence_from_correlation_matrix_file_example.py | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 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 79f6df75..ad990fdc 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 @@ -1,6 +1,7 @@ #!/usr/bin/env python import gudhi +import sys import argparse """This file is part of the Gudhi Library. The Gudhi library @@ -37,23 +38,29 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from ' '- 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("-e", "--max_edge_length", type=float, default=0.5) +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("RipsComplex creation from correlation matrix read in a csv file") -message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) +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[0]))] for i in range(len(correlation_matrix))] -rips_complex = gudhi.RipsComplex(distance_matrix=distance_matrix, max_edge_length=args.max_edge_length) +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()) @@ -64,6 +71,9 @@ 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(diag, band_boot=args.band_boot) + pplot = gudhi.plot_persistence_diagram(invert_diag, band_boot=args.band_boot) pplot.show() -- cgit v1.2.3