1 files changed, 105 insertions, 0 deletions
diff --git a/src/python/example/alpha_rips_persistence_bottleneck_distance.py b/src/python/example/alpha_rips_persistence_bottleneck_distance.py
new file mode 100755
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+++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py
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+#!/usr/bin/env python
+
+import gudhi
+import argparse
+import math
+
+""" 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
+
+    Copyright (C) 2016 Inria
+
+    Modification(s):
+      - YYYY/MM Author: Description of the modification
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 Inria"
+__license__ = "MIT"
+
+parser = argparse.ArgumentParser(
+    description="AlphaComplex and RipsComplex "
+    "persistence creation from points read in "
+    "a OFF file. Bottleneck distance computation"
+    " on each dimension",
+    epilog="Example: "
+    "example/alpha_rips_persistence_bottleneck_distance.py "
+    "-f ../data/points/tore3D_1307.off -t 0.15 -d 3",
+)
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-t", "--threshold", type=float, default=0.5)
+parser.add_argument("-d", "--max_dimension", type=int, default=1)
+
+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(
+            points=point_cloud, max_edge_length=args.threshold
+        )
+
+        rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
+
+        message = "Number of simplices=" + repr(rips_stree.num_simplices())
+        print(message)
+
+        rips_diag = rips_stree.persistence()
+
+        print("#####################################################################")
+        print("AlphaComplex creation from points read in a OFF file")
+
+        message = "AlphaComplex with max_edge_length=" + repr(args.threshold)
+        print(message)
+
+        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())
+        print(message)
+
+        alpha_diag = alpha_stree.persistence()
+
+        max_b_distance = 0.0
+        for dim in range(args.max_dimension):
+            # Alpha persistence values needs to be transform because filtration
+            # values are alpha square values
+            funcs = [math.sqrt, math.sqrt]
+            alpha_intervals = []
+            for interval in alpha_stree.persistence_intervals_in_dimension(dim):
+                alpha_intervals.append(
+                    map(lambda func, value: func(value), funcs, interval)
+                )
+
+            rips_intervals = rips_stree.persistence_intervals_in_dimension(dim)
+            bottleneck_distance = gudhi.bottleneck_distance(
+                rips_intervals, alpha_intervals
+            )
+            message = (
+                "In dimension "
+                + repr(dim)
+                + ", bottleneck distance = "
+                + repr(bottleneck_distance)
+            )
+            print(message)
+            max_b_distance = max(bottleneck_distance, max_b_distance)
+
+        print(
+            "================================================================================"
+        )
+        message = "Bottleneck distance is " + repr(max_b_distance)
+        print(message)
+
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()