diff options
author | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2019-06-26 16:59:58 +0200 |
---|---|---|
committer | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2019-06-26 16:59:58 +0200 |
commit | fd47a2d926e78d3b83e79da3c959fb73809d09e4 (patch) | |
tree | d440223947ae58fa06d15c575f08023902bad898 /src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py | |
parent | 2ffd579440e6f0158588f8fa905e2f1dc49a5158 (diff) |
Format Python files with black
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 | 47 |
1 files changed, 31 insertions, 16 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 98be0123..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 @@ -18,22 +18,28 @@ __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2017 Inria" __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 = 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) @@ -48,12 +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()) @@ -65,7 +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) |