Add Windows and CGAL_HEADER_ONLY cythonization support

Add OFF reader interfaces (required by Euclidean witness complex)
Add Euclidean_witness_complex



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2186 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4d780f05c3409bea47a81e4377dbaf509b9e718c

2 files changed, 78 insertions, 56 deletions

diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
new file mode 100755
index 00000000..7f04a98e
--- /dev/null
+++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+
+import gudhi
+import argparse
+
+"""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='EuclideanWitnessComplex creation from '
+                                 'points read in a OFF file.',
+                                 epilog='Example: '
+                                 'example/witness_complex_diagram_persistence_from_off_file_example.py '
+                                 '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2'
+                                 '- Constructs a alpha complex with the '
+                                 'points from the given OFF file.')
+parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
+parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
+parser.add_argument("-d", "--limit_dimension", type=int, required=True)
+parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
+
+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'):
+        print("#####################################################################")
+        print("EuclideanWitnessComplex creation from points read in a OFF file")
+
+        witnesses = gudhi.read_off(off_file=args.file)
+        landmarks = gudhi.pick_n_random_points(points=witnesses, nb_points=args.number_of_landmarks)
+
+        message = "EuclideanWitnessComplex with max_edge_length=" + repr(args.max_alpha_square) + \
+            " - Number of landmarks=" + repr(args.number_of_landmarks)
+        print(message)
+
+        witness_complex = gudhi.EuclideanWitnessComplex(witnesses=witnesses, landmarks=landmarks)
+        simplex_tree = witness_complex.create_simplex_tree(max_alpha_square=args.max_alpha_square,
+            limit_dimension=args.limit_dimension)
+
+        message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+        print(message)
+
+        diag = simplex_tree.persistence()
+
+        print("betti_numbers()=")
+        print(simplex_tree.betti_numbers())
+
+        if args.no_diagram == False:
+            gudhi.diagram_persistence(diag)
+
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/example/witness_complex_from_file_example.py b/src/cython/example/witness_complex_from_file_example.py
deleted file mode 100755
index 82a5b49a..00000000
--- a/src/cython/example/witness_complex_from_file_example.py
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env python
-
-import gudhi
-import pandas
-import argparse
-
-"""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"
-
-print("#####################################################################")
-print("WitnessComplex creation from points read in a file")
-
-parser = argparse.ArgumentParser(description='WitnessComplex creation from '
-                                 'points read in a file.',
-                                 epilog='Example: '
-                                 'example/witness_complex_from_file_example.py'
-                                 ' data/2000_random_points_on_3D_Torus.csv '
-                                 '- Constructs a witness complex with the '
-                                 'points from the given file. File format '
-                                 'is X1, X2, ..., Xn')
-parser.add_argument('file', type=argparse.FileType('r'))
-args = parser.parse_args()
-
-points = pandas.read_csv(args.file, header=None)
-
-print("WitnessComplex with number_of_landmarks=100")
-
-witness_complex = gudhi.WitnessComplex(points=points.values,
-                                       number_of_landmarks=100)
-
-witness_complex.initialize_filtration()
-
-print("filtered_tree=", witness_complex.get_filtered_tree())