From 6f6a2f71b6ae33cd37719ad13006699ad78fcc84 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 3 Feb 2017 11:57:56 +0000
Subject: Automatic examples documentation page generation
 alpha_rips_persistence_bottleneck_distance example for python Add
 intervals_in_dim function for simplex tree

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2055 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 460fbe5db9f0c08776952106e729a21460bec36f
---
 .../alpha_rips_persistence_bottleneck_distance.py  | 102 +++++++++++++++++++++
 1 file changed, 102 insertions(+)
 create mode 100755 src/cython/example/alpha_rips_persistence_bottleneck_distance.py

(limited to 'src/cython/example')

diff --git a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py
new file mode 100755
index 00000000..04a59b44
--- /dev/null
+++ b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py
@@ -0,0 +1,102 @@
+#!/usr/bin/env python
+
+import gudhi
+import argparse
+import math
+
+"""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) 2016 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) 2016 INRIA"
+__license__ = "GPL v3"
+
+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()
+print(repr(float('inf')))
+print(repr(math.sqrt(float('inf'))))
+with open(args.file, 'r') as f:
+    first_line = f.readline()
+    if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
+        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,
+                                         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(off_file=args.file)
+        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.intervals_in_dim(dim):
+                alpha_intervals.append(map(lambda func,value: func(value), funcs, interval))
+
+            rips_intervals = rips_stree.intervals_in_dim(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()
-- 
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