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

3 files changed, 121 insertions, 14 deletions

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)