Remove pandas examples and use of OFF files interfaces to be more consistent (pandas interface is not that hard to be done)

Add of distance matrix in Rips


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2081 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3a3b24f0824eed2710edb5bf17d120039973bf62

9 files changed, 329 insertions, 61 deletions

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 8723d731..6f7d5de7 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -132,6 +132,7 @@ if(PYTHON_PATH AND CYTHON_PATH)
       file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt")
       file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
       file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+      file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
       # Persistence graphical tools examples
       file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
       file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
diff --git a/src/cython/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx
index 7e04ca4b..6bfb4482 100644
--- a/src/cython/cython/rips_complex.pyx
+++ b/src/cython/cython/rips_complex.pyx
@@ -33,9 +33,9 @@ __license__ = "GPL v3"
 
 cdef extern from "Rips_complex_interface.h" namespace "Gudhi":
     cdef cppclass Rips_complex_interface "Gudhi::rips_complex::Rips_complex_interface":
-        Rips_complex_interface(vector[vector[double]] points, double threshold)
+        Rips_complex_interface(vector[vector[double]] values, double threshold, bool euclidean)
         # bool from_file is a workaround for cython to find the correct signature
-        Rips_complex_interface(string off_file, double threshold, bool from_file)
+        Rips_complex_interface(string file_name, double threshold, bool euclidean, bool from_file)
         void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max)
 
 # RipsComplex python interface
@@ -49,9 +49,12 @@ cdef class RipsComplex:
     cdef Rips_complex_interface * thisptr
 
     # Fake constructor that does nothing but documenting the constructor
-    def __init__(self, points=[], off_file='', max_edge_length=float('inf')):
+    def __init__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')):
         """RipsComplex constructor.
 
+        :param max_edge_length: Rips value.
+        :type max_edge_length: int
+
         :param points: A list of points in d-Dimension.
         :type points: list of list of double
 
@@ -60,21 +63,44 @@ cdef class RipsComplex:
         :param off_file: An OFF file style name.
         :type off_file: string
 
-        :param max_edge_length: Rips value.
-        :type max_edge_length: int
+        Or
+
+        :param distance_matrix: A distance matrix (full square or lower
+        triangular).
+        :type points: list of list of double
+
+        Or
+
+        :param csv_file: A csv file style name containing a full square or a
+        lower triangular distance matrix.
+        :type csv_file: string
         """
 
     # The real cython constructor
-    def __cinit__(self, points=[], off_file='', max_edge_length=float('inf')):
+    def __cinit__(self, points=None, off_file='', distance_matrix=None, csv_file='', max_edge_length=float('inf')):
         if off_file is not '':
             if os.path.isfile(off_file):
                 self.thisptr = new Rips_complex_interface(off_file,
                                                           max_edge_length,
+                                                          True,
                                                           True)
             else:
                 print("file " + off_file + " not found.")
+        elif csv_file is not '':
+            if os.path.isfile(csv_file):
+                self.thisptr = new Rips_complex_interface(csv_file,
+                                                          max_edge_length,
+                                                          False,
+                                                          True)
+            else:
+                print("file " + csv_file + " not found.")
+        elif distance_matrix is not None:
+            self.thisptr = new Rips_complex_interface(distance_matrix, max_edge_length, False)
         else:
-            self.thisptr = new Rips_complex_interface(points, max_edge_length)
+            if points is None:
+                # Empty Rips construction
+                points=[]
+            self.thisptr = new Rips_complex_interface(points, max_edge_length, True)
 
 
     def __dealloc__(self):
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index 12d35821..20d97b3c 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -112,8 +112,9 @@ The following examples require the `Matplotlib <http://matplotlib.org>`_:
     * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>`
     * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
-    * :download:`rips_complex_diagram_persistence_with_pandas_interface_example.py <../example/rips_complex_diagram_persistence_with_pandas_interface_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>`
+    * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>`
     * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
 
 Numpy
@@ -130,6 +131,7 @@ The following examples require the `NumPy <http://numpy.org>`_:
     * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>`
     * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
-    * :download:`rips_complex_diagram_persistence_with_pandas_interface_example.py <../example/rips_complex_diagram_persistence_with_pandas_interface_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>`
+    * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>`
     * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst
index 4ca4805d..d264a011 100644
--- a/src/cython/doc/persistent_cohomology_user.rst
+++ b/src/cython/doc/persistent_cohomology_user.rst
@@ -101,8 +101,9 @@ We provide several example files: run these examples with -h for details on thei
 
     * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>`
     * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
-    * :download:`rips_complex_diagram_persistence_with_pandas_interface_example.py <../example/rips_complex_diagram_persistence_with_pandas_interface_example.py>`
+    * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>`
+    * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>`
     * :download:`random_cubical_complex_persistence_example.py <../example/random_cubical_complex_persistence_example.py>`
     * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
 
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index be9481de..a5d17e19 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -38,16 +38,16 @@ set with :math:`max(filtration(4,5), filtration(4,6), filtration(5,6))`. And so
 If the Rips_complex interfaces are not detailed enough for your need, please refer to rips_persistence_step_by_step.cpp
 example, where the graph construction over the Simplex_tree is more detailed.
 
-Point cloud and distance function
----------------------------------
+Point cloud
+-----------
 
-Example from a point cloud and a distance function
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Example from a point cloud
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-This example builds the one skeleton graph from the given points, threshold value, and distance function. Then it
-creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
+This example builds the one skeleton graph from the given points, and max_edge_length value.
+Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
 
-Then, it is asked to display information about the simplicial complex.
+Finally, it is asked to display information about the simplicial complex.
 
 .. testcode::
 
@@ -63,7 +63,8 @@ Then, it is asked to display information about the simplicial complex.
     for filtered_value in simplex_tree.get_filtered_tree():
         print(filtered_value)
 
-The output is:
+When launching (Rips maximal distance between 2 points is 12.0, is expanded
+until dimension 1 - one skeleton graph in other words), the output is:
 
 .. testoutput::
 
@@ -90,10 +91,11 @@ The output is:
 Example from OFF file
 ^^^^^^^^^^^^^^^^^^^^^
 
-This example builds the :doc:`Rips_complex <rips_complex_ref>` from the given points in an OFF file, threshold value,
-and distance function. Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
+This example builds the :doc:`Rips_complex <rips_complex_ref>` from the given
+points in an OFF file, and max_edge_length value.
+Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
 
-Then, it is asked to display information about the Rips complex.
+Finally, it is asked to display information about the Rips complex.
 
 
 .. testcode::
@@ -131,3 +133,105 @@ the program output is:
     ([0, 3], 9.433981132056603)
     ([4, 6], 9.486832980505138)
     ([3, 6], 11.0)
+
+Distance matrix
+---------------
+
+Example from a distance matrix
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This example builds the one skeleton graph from the given distance matrix, and max_edge_length value.
+Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
+
+Finally, it is asked to display information about the simplicial complex.
+
+.. testcode::
+
+    import gudhi
+    rips_complex = gudhi.RipsComplex(distance_matrix=[[],
+                                                      [6.0827625303],
+                                                      [5.8309518948, 6.7082039325],
+                                                      [9.4339811321, 6.3245553203, 5],
+                                                      [13.0384048104, 15.6524758425, 8.94427191, 12.0415945788],
+                                                      [18.0277563773, 19.6468827044, 13.152946438, 14.7648230602, 5.3851648071],
+                                                      [17.88854382, 17.1172427686, 12.0830459736, 11, 9.4868329805, 7.2801098893]],
+                                     max_edge_length=12.0)
+
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
+    result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+        repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+        repr(simplex_tree.num_vertices()) + ' vertices.'
+    print(result_str)
+    for filtered_value in simplex_tree.get_filtered_tree():
+        print(filtered_value)
+
+When launching (Rips maximal distance between 2 points is 12.0, is expanded
+until dimension 1 - one skeleton graph in other words), the output is:
+
+.. testoutput::
+
+    Rips complex is of dimension 1 - 18 simplices - 7 vertices.
+    ([0], 0.0)
+    ([1], 0.0)
+    ([2], 0.0)
+    ([3], 0.0)
+    ([4], 0.0)
+    ([5], 0.0)
+    ([6], 0.0)
+    ([2, 3], 5.0)
+    ([4, 5], 5.3851648071)
+    ([0, 2], 5.8309518948)
+    ([0, 1], 6.0827625303)
+    ([1, 3], 6.3245553203)
+    ([1, 2], 6.7082039325)
+    ([5, 6], 7.2801098893)
+    ([2, 4], 8.94427191)
+    ([0, 3], 9.4339811321)
+    ([4, 6], 9.4868329805)
+    ([3, 6], 11.0)
+
+Example from OFF file
+^^^^^^^^^^^^^^^^^^^^^
+
+This example builds the :doc:`Rips_complex <rips_complex_ref>` from the given
+points in an OFF file, and max_edge_length value.
+Then it creates a :doc:`Simplex_tree <simplex_tree_ref>` with it.
+
+Finally, it is asked to display information about the Rips complex.
+
+
+.. testcode::
+
+    import gudhi
+    rips_complex = gudhi.RipsComplex(csv_file='full_square_distance_matrix.csv', max_edge_length=12.0)
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
+    result_str = 'Rips complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+        repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+        repr(simplex_tree.num_vertices()) + ' vertices.'
+    print(result_str)
+    for filtered_value in simplex_tree.get_filtered_tree():
+        print(filtered_value)
+
+the program output is:
+
+.. testoutput::
+
+    Rips complex is of dimension 1 - 18 simplices - 7 vertices.
+    ([0], 0.0)
+    ([1], 0.0)
+    ([2], 0.0)
+    ([3], 0.0)
+    ([4], 0.0)
+    ([5], 0.0)
+    ([6], 0.0)
+    ([2, 3], 5.0)
+    ([4, 5], 5.3851648071)
+    ([0, 2], 5.8309518948)
+    ([0, 1], 6.0827625303)
+    ([1, 3], 6.3245553203)
+    ([1, 2], 6.7082039325)
+    ([5, 6], 7.2801098893)
+    ([2, 4], 8.94427191)
+    ([0, 3], 9.4339811321)
+    ([4, 6], 9.4868329805)
+    ([3, 6], 11.0)
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
new file mode 100755
index 00000000..2b726f90
--- /dev/null
+++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -0,0 +1,71 @@
+#!/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='RipsComplex creation from '
+                                 'a distance matrix read in a OFF 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.')
+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('--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("RipsComplex creation from distance matrix read in a csv file")
+        
+        message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+        print(message)
+        
+        rips_complex = gudhi.RipsComplex(off_file=args.file, 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:
+            gudhi.diagram_persistence(diag)
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
index 8af1b767..eb1c4ed5 100755
--- a/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import gudhi
-import pandas
 import argparse
 
 """This file is part of the Gudhi Library. The Gudhi library
@@ -30,40 +29,43 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
-print("#####################################################################")
-print("RipsComplex creation from points read in a file")
-
 parser = argparse.ArgumentParser(description='RipsComplex creation from '
-                                 'points read in a file.',
+                                 'points read in a OFF file.',
                                  epilog='Example: '
-                                 'example/rips_complex_diagram_persistence_with_pandas_interface_example.py '
-                                 '../data/2000_random_points_on_3D_Torus.csv '
-                                 '- Constructs a rips complex with the '
-                                 'points from the given file. File format '
-                                 'is X1, X2, ..., Xn')
+                                 'example/rips_complex_diagram_persistence_from_off_file_example.py '
+                                 '-f ../data/points/tore3D_300.off -a 0.6'
+                                 '- Constructs a Rips complex with the '
+                                 'points from the given OFF 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("-e", "--max_edge_length", type=float, default=0.5)
+parser.add_argument("-d", "--max_dimension", type=int, default=1)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
 
-points = pandas.read_csv(args.file, header=None)
-
-message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
-print(message)
-
-rips_complex = gudhi.RipsComplex(points=points.values,
-                                 max_edge_length=args.max_edge_length)
-
-simplex_tree = rips_complex.create_simplex_tree(max_dimension=len(points.values[0]))
-
-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)
+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.max_edge_length)
+        print(message)
+        
+        rips_complex = gudhi.RipsComplex(off_file=args.file, 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:
+            gudhi.diagram_persistence(diag)
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
index 7e897b1d..9295906c 100644
--- a/src/cython/include/Rips_complex_interface.h
+++ b/src/cython/include/Rips_complex_interface.h
@@ -27,6 +27,7 @@
 #include <gudhi/Rips_complex.h>
 #include <gudhi/Points_off_io.h>
 #include <gudhi/distance_functions.h>
+#include <gudhi/reader_utils.h>
 
 #include "Simplex_tree_interface.h"
 
@@ -41,17 +42,34 @@ namespace rips_complex {
 
 class Rips_complex_interface {
   using Point_d = std::vector<double>;
+  using Distance_matrix = std::vector<std::vector<Simplex_tree_interface<>::Filtration_value>>;
 
  public:
-  Rips_complex_interface(std::vector<std::vector<double>>&points, double threshold) {
-    rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(points, threshold,
-                                                                                 Euclidean_distance());
+  Rips_complex_interface(std::vector<std::vector<double>>&values, double threshold, bool euclidean) {
+    if (euclidean) {
+      // Rips construction where values is a vector of points
+      rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(values, threshold,
+                                                                                   Euclidean_distance());
+    } else {
+      // Rips construction where values is a distance matrix
+      rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(values, threshold);
+
+    }
   }
 
-  Rips_complex_interface(std::string off_file_name, double threshold, bool from_file = true) {
-    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
-    rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(off_reader.get_point_cloud(),
-                                                                                 threshold, Euclidean_distance());
+  Rips_complex_interface(std::string file_name, double threshold, bool euclidean, bool from_file = true) {
+    if (euclidean) {
+      // Rips construction where file_name is an OFF file
+      Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+      rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(off_reader.get_point_cloud(),
+                                                                                   threshold, Euclidean_distance());
+    } else {
+      // Rips construction where values is a distance matrix
+      Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
+      rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(distances, threshold);
+
+    }
+
   }
 
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) {
diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py
index 687e8529..464c69e5 100755
--- a/src/cython/test/test_rips_complex.py
+++ b/src/cython/test/test_rips_complex.py
@@ -1,4 +1,5 @@
 from gudhi import RipsComplex
+from math import sqrt
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -31,7 +32,7 @@ def test_empty_rips():
     rips_complex = RipsComplex()
     assert rips_complex.__is_defined() == True
 
-def test_rips():
+def test_rips_from_points():
     point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
     rips_complex = RipsComplex(points=point_list, max_edge_length=42)
 
@@ -55,7 +56,7 @@ def test_rips():
            [([0, 1], 1.0), ([0, 2], 1.0),
             ([0, 3], 1.4142135623730951)]
 
-def test_filtered_rips():
+def test_filtered_rips_from_points():
     point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
     filtered_rips = RipsComplex(points=point_list, max_edge_length=1.0)
 
@@ -66,3 +67,45 @@ def test_filtered_rips():
 
     assert simplex_tree.num_simplices() == 8
     assert simplex_tree.num_vertices() == 4
+
+def test_rips_from_distance_matrix():
+    distance_matrix = [[0],
+                       [1, 0],
+                       [1, sqrt(2), 0],
+                       [sqrt(2), 1, 1, 0]]
+    rips_complex = RipsComplex(distance_matrix=distance_matrix, max_edge_length=42)
+
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=1)
+
+    assert simplex_tree.__is_defined() == True
+    assert simplex_tree.__is_persistence_defined() == False
+
+    assert simplex_tree.num_simplices() == 10
+    assert simplex_tree.num_vertices() == 4
+
+    assert simplex_tree.get_filtered_tree() == \
+           [([0], 0.0), ([1], 0.0), ([2], 0.0), ([3], 0.0),
+            ([0, 1], 1.0), ([0, 2], 1.0), ([1, 3], 1.0),
+            ([2, 3], 1.0), ([1, 2], 1.4142135623730951),
+            ([0, 3], 1.4142135623730951)]
+    assert simplex_tree.get_star_tree([0]) == \
+           [([0], 0.0), ([0, 1], 1.0), ([0, 2], 1.0),
+            ([0, 3], 1.4142135623730951)]
+    assert simplex_tree.get_coface_tree([0], 1) == \
+           [([0, 1], 1.0), ([0, 2], 1.0),
+            ([0, 3], 1.4142135623730951)]
+
+def test_filtered_rips_from_distance_matrix():
+    distance_matrix = [[0],
+                       [1, 0],
+                       [1, sqrt(2), 0],
+                       [sqrt(2), 1, 1, 0]]
+    filtered_rips = RipsComplex(distance_matrix=distance_matrix, max_edge_length=1.0)
+
+    simplex_tree = filtered_rips.create_simplex_tree(max_dimension=1)
+
+    assert simplex_tree.__is_defined() == True
+    assert simplex_tree.__is_persistence_defined() == False
+
+    assert simplex_tree.num_simplices() == 8
+    assert simplex_tree.num_vertices() == 4