Merge last trunk modifications

Comment some bad code
Try to cythonize rips from correlation matrix


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2858 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3b9bcdfdeae247ed5486e20cb62f2812fdd14b0d

3 files changed, 71 insertions, 4 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
new file mode 100755
index 00000000..79f6df75
--- /dev/null
+++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -0,0 +1,69 @@
+#!/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) 2017 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) 2017 INRIA"
+__license__ = "GPL v3"
+
+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("-e", "--max_edge_length", 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()
+
+print("#####################################################################")
+print("RipsComplex creation from correlation matrix read in a csv file")
+
+message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+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)
+simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_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:
+    pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+    pplot.show()
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index fa82a2f3..c8aac240 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -30,12 +30,12 @@ __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
 parser = argparse.ArgumentParser(description='RipsComplex creation from '
-                                 'a distance matrix read in a OFF file.',
+                                 'a distance matrix read in a csv file.',
                                  epilog='Example: '
                                  'example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py '
                                  '-f ../data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3'
                                  '- Constructs a Rips complex with the '
-                                 'points from the given OFF file.')
+                                 'distance 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("-d", "--max_dimension", type=int, default=1)
diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py
index 831d9da8..51a60e73 100755
--- a/src/cython/example/simplex_tree_example.py
+++ b/src/cython/example/simplex_tree_example.py
@@ -48,8 +48,6 @@ if st.insert([0, 1, 2], filtration=4.0):
 else:
     print("Not inserted...")
 
-# FIXME: Remove this line
-st.set_dimension(3)
 print("dimension=", st.dimension())
 
 st.initialize_filtration()