message: Do like C++ example
diff: #!/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()
  