Merge branch 'master' into simplex_tree_insert_duplicated_vertices_fix_vincent

9 files changed, 102 insertions, 46 deletions

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 97859c98..480332d7 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -215,12 +215,7 @@ if(PYTHONINTERP_FOUND)
     add_custom_target(cython ALL DEPENDS gudhi.so
                       COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
 
-    # For installation purpose
-    # TODO(VR) : files matching pattern mechanism is copying all cython directory
-    install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}" DESTINATION "${PYTHON_SITE_PACKAGES}/" FILES_MATCHING
-        PATTERN "*.so"
-        PATTERN "*.dylib"
-        PATTERN "*.pyd")
+    install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
 
     # Test examples
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/cython/cython/tangential_complex.pyx b/src/cython/cython/tangential_complex.pyx
index 4bb07076..293ef8cb 100644
--- a/src/cython/cython/tangential_complex.pyx
+++ b/src/cython/cython/tangential_complex.pyx
@@ -36,6 +36,7 @@ cdef extern from "Tangential_complex_interface.h" namespace "Gudhi":
         Tangential_complex_interface(int intrisic_dim, vector[vector[double]] points)
         # bool from_file is a workaround for cython to find the correct signature
         Tangential_complex_interface(int intrisic_dim, string off_file, bool from_file)
+        void compute_tangential_complex() except +
         vector[double] get_point(unsigned vertex)
         unsigned number_of_vertices()
         unsigned number_of_simplices()
@@ -43,6 +44,7 @@ cdef extern from "Tangential_complex_interface.h" namespace "Gudhi":
         unsigned number_of_inconsistent_stars()
         void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree)
         void fix_inconsistencies_using_perturbation(double max_perturb, double time_limit)
+        void set_max_squared_edge_length(double max_squared_edge_length)
 
 # TangentialComplex python interface
 cdef class TangentialComplex:
@@ -92,6 +94,17 @@ cdef class TangentialComplex:
          """
         return self.thisptr != NULL
 
+    def compute_tangential_complex(self):
+        """This function computes the tangential complex.
+
+        Raises:
+            ValueError: In debug mode, if the computed star dimension is too
+                low. Try to set a bigger maximal edge length value with
+                :func:`~gudhi.Tangential_complex.set_max_squared_edge_length`
+                if this happens.
+        """
+        self.thisptr.compute_tangential_complex()
+
     def get_point(self, vertex):
         """This function returns the point corresponding to a given vertex.
 
@@ -152,3 +165,16 @@ cdef class TangentialComplex:
         """
         self.thisptr.fix_inconsistencies_using_perturbation(max_perturb,
                                                             time_limit)
+
+    def set_max_squared_edge_length(self, max_squared_edge_length):
+        """Sets the maximal possible squared edge length for the edges in the
+        triangulations.
+
+        :param max_squared_edge_length: Maximal possible squared edge length.
+        :type max_squared_edge_length: double
+
+        If the maximal edge length value is too low
+        :func:`~gudhi.Tangential_complex.compute_tangential_complex`
+        will throw an exception in debug mode.
+        """
+        self.thisptr.set_max_squared_edge_length(max_squared_edge_length)
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index 040f6b4a..855dea44 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -7,24 +7,23 @@ Installation
 
 Compiling
 *********
-The library uses c++11 and requires `Boost <https://www.boost.org/>`_ ≥ 1.56.0
-and `CMake <https://www.cmake.org/>`_   ≥ 3.1.
+The library uses c++11 and requires `Boost <https://www.boost.org/>`_ ≥ 1.56.0,
+`CMake <https://www.cmake.org/>`_   ≥ 3.1  to generate makefiles, and
+`Cython <https://www.cython.org/>`_ to compile the GUDHI Python module.
 It is a multi-platform library and compiles on Linux, Mac OSX and Visual
 Studio 2015.
-It also requires cmake to generate makefiles, and cython to compile the
-library.
 
 On `Windows <https://wiki.python.org/moin/WindowsCompilers>`_ , only Python
 3.5 and 3.6 are available because of the required Visual Studio version.
 
-On other systems, if you have several Python/cython installed, the version 2.X
+On other systems, if you have several Python/Cython installed, the version 2.X
 will be used by default, but you can force it by adding
 :code:`-DPython_ADDITIONAL_VERSIONS=3` to the cmake command.
 
-GUDHI Cythonization
-===================
+GUDHI Python module compilation
+===============================
 
-To build the GUDHI cython module, run the following commands in a terminal:
+To build the GUDHI Python module, run the following commands in a terminal:
 
 .. code-block:: bash
 
@@ -32,7 +31,28 @@ To build the GUDHI cython module, run the following commands in a terminal:
     mkdir build
     cd build/
     cmake ..
-    make cython
+    cd cython
+    make
+
+GUDHI Python module installation
+================================
+
+Once the compilation succeeds, one can add the GUDHI Python module path to the
+PYTHONPATH:
+
+.. code-block:: bash
+
+    # For windows, you have to set PYTHONPATH environment variable
+    export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython'
+
+Or install it definitely in your Python packages folder:
+
+.. code-block:: bash
+
+    cd /path-to-gudhi/build/cython
+    # May require sudo or administrator privileges
+    make install
+
 
 Test suites
 ===========
@@ -45,7 +65,7 @@ following command in a terminal:
     cd /path-to-gudhi/build/cython
     # For windows, you have to set PYTHONPATH environment variable
     export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython'
-    ctest -R py_test
+    make test
 
 Debugging issues
 ================
@@ -54,7 +74,7 @@ If tests fail, please check your PYTHONPATH and try to :code:`import gudhi`
 and check the errors.
 The problem can come from a third-party library bad link or installation.
 
-If :code:`import gudhi` succeeds, please have a look to debug informations:
+If :code:`import gudhi` succeeds, please have a look to debug information:
 
 .. code-block:: python
 
@@ -105,13 +125,17 @@ A complete configuration would be :
 Documentation
 =============
 
-To build the documentation, `sphinx-doc <http://http://www.sphinx-doc.org>`_ is
-required. Please refer to *conf.py* file to see which
-`sphinx-doc <http://http://www.sphinx-doc.org>`_ modules are required to
-generate the documentation. Run the following commands in a terminal:
+To build the documentation, `sphinx-doc <http://www.sphinx-doc.org>`_ and
+`sphinxcontrib-bibtex <https://sphinxcontrib-bibtex.readthedocs.io>`_ are
+required. As the documentation is auto-tested, `CGAL`_, `Eigen3`_,
+`Matplotlib`_, `NumPy`_ and `SciPy`_ are also mandatory to build the
+documentation.
+
+Run the following commands in a terminal:
 
 .. code-block:: bash
 
+    cd /path-to-gudhi/build/cython
     make sphinx
 
 Optional third-party library
@@ -127,7 +151,7 @@ The :doc:`Alpha complex </alpha_complex_user>`,
 C++ library which provides easy access to efficient and reliable geometric
 algorithms.
 
-Having CGAL,  the Computational Geometry Algorithms Library, version 4.7.0 or
+Having CGAL, the Computational Geometry Algorithms Library, version 4.7.0 or
 higher installed is recommended. The procedure to install this library
 according to your operating system is detailed
 `here <http://doc.cgal.org/latest/Manual/installation.html>`_.
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index e814b4c3..1d340dbe 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -50,8 +50,8 @@ by more than the length used to define "too close".
 A more general technique is to use a sparse approximation of the Rips
 introduced by Don Sheehy :cite:`sheehy13linear`. We are using the version
 described in :cite:`buchet16efficient` (except that we multiply all filtration
-values by 2, to match the usual Rips complex), which proves a
-:math:`\frac{1+\varepsilon}{1-\varepsilon}`-interleaving, although in practice the
+values by 2, to match the usual Rips complex). :cite:`cavanna15geometric` proves
+a :math:`\frac{1}{1-\varepsilon}`-interleaving, although in practice the
 error is usually smaller.  A more intuitive presentation of the idea is
 available in :cite:`cavanna15geometric`, and in a video
 :cite:`cavanna15visualizing`. Passing an extra argument `sparse=0.3` at the
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index 5ce69e86..ebfe1e29 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -23,8 +23,10 @@ What is a Tangential Complex?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Let us start with the description of the Tangential complex of a simple
-example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
-:math:`P` located on a curve embedded in 2D.
+example, with :math:`k = 1` and :math:`d = 2`. The point set
+:math:`\mathscr P` is located on a closed curve embedded in 2D.
+Only 4 points will be displayed (more are required for PCA) to simplify the
+figures.
 
 .. figure:: ../../doc/Tangential_complex/tc_example_01.png
     :alt: The input
@@ -32,8 +34,7 @@ example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
 
     The input
 
-For each point :math:`p`, estimate its tangent subspace :math:`T_p` (e.g.
-using PCA). 
+For each point :math:`P`, estimate its tangent subspace :math:`T_P` using PCA.
 
 .. figure:: ../../doc/Tangential_complex/tc_example_02.png
     :alt: The estimated normals
@@ -43,8 +44,8 @@ using PCA).
 
 
 Let us add the Voronoi diagram of the points in orange. For each point
-:math:`p`, construct its star in the Delaunay triangulation of :math:`P`
-restricted to :math:`T_p`.
+:math:`P`, construct its star in the Delaunay triangulation of
+:math:`\mathscr P` restricted to :math:`T_P`.
 
 .. figure:: ../../doc/Tangential_complex/tc_example_03.png
     :alt: The Voronoi diagram
@@ -72,7 +73,7 @@ Let us take the same example.
 
     Before
 
-Let us slightly move the tangent subspace :math:`T_q`
+Let us slightly move the tangent subspace :math:`T_Q`
 
 .. figure:: ../../doc/Tangential_complex/tc_example_07_after.png
     :alt: After
@@ -128,6 +129,7 @@ This example builds the Tangential complex of point set read in an OFF file.
     import gudhi
     tc = gudhi.TangentialComplex(intrisic_dim = 1,
         off_file=gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off')
+    tc.compute_tangential_complex()
     result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \
         ' simplices - ' + repr(tc.num_vertices()) + ' vertices.'
     print(result_str)
@@ -175,6 +177,7 @@ simplices.
    import gudhi
    tc = gudhi.TangentialComplex(intrisic_dim = 1,
        points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]])
+   tc.compute_tangential_complex()
    result_str = 'Tangential contains ' + repr(tc.num_vertices()) + ' vertices.'
    print(result_str)
 
diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
index 0f8f5e80..536517d1 100755
--- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
+++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -50,6 +50,7 @@ with open(args.file, 'r') as f:
         print("TangentialComplex creation from points read in a OFF file")
         
         tc = gudhi.TangentialComplex(intrisic_dim = args.intrisic_dim, off_file=args.file)
+        tc.compute_tangential_complex()
         st = tc.create_simplex_tree()
     
         message = "Number of simplices=" + repr(st.num_simplices())
diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
index 1a6e2477..40aff299 100644
--- a/src/cython/include/Rips_complex_interface.h
+++ b/src/cython/include/Rips_complex_interface.h
@@ -54,23 +54,17 @@ class Rips_complex_interface {
   }
 
   void init_points_sparse(const std::vector<std::vector<double>>& points, double threshold, double epsilon) {
-    sparse_rips_complex_.emplace(points, Gudhi::Euclidean_distance(), epsilon);
-    threshold_ = threshold;
+    sparse_rips_complex_.emplace(points, Gudhi::Euclidean_distance(), epsilon, -std::numeric_limits<double>::infinity(), threshold);
   }
   void init_matrix_sparse(const std::vector<std::vector<double>>& matrix, double threshold, double epsilon) {
-    sparse_rips_complex_.emplace(matrix, epsilon);
-    threshold_ = threshold;
+    sparse_rips_complex_.emplace(matrix, epsilon, -std::numeric_limits<double>::infinity(), threshold);
   }
 
   void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, int dim_max) {
     if (rips_complex_)
       rips_complex_->create_complex(*simplex_tree, dim_max);
-    else {
+    else
       sparse_rips_complex_->create_complex(*simplex_tree, dim_max);
-      // This pruning should be done much earlier! It isn't that useful for sparse Rips,
-      // but it would be inconsistent not to do it.
-      simplex_tree->prune_above_filtration(threshold_);
-    }
     simplex_tree->initialize_filtration();
   }
 
@@ -79,7 +73,6 @@ class Rips_complex_interface {
   // Anyway, storing a graph would make more sense. Or changing the interface completely so there is no such storage.
   boost::optional<Rips_complex<Simplex_tree_interface<>::Filtration_value>> rips_complex_;
   boost::optional<Sparse_rips_complex<Simplex_tree_interface<>::Filtration_value>> sparse_rips_complex_;
-  double threshold_;
 };
 
 }  // namespace rips_complex
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index 71418886..c4ddbdbe 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -49,8 +49,6 @@ class Tangential_complex_interface {
     Dynamic_kernel k;
 
     tangential_complex_ = new TC(points, intrisic_dim, k);
-    tangential_complex_->compute_tangential_complex();
-    num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
   }
 
   Tangential_complex_interface(int intrisic_dim, const std::string& off_file_name, bool from_file = true) {
@@ -60,14 +58,17 @@ class Tangential_complex_interface {
     std::vector<Point_d> points = off_reader.get_point_cloud();
 
     tangential_complex_ = new TC(points, intrisic_dim, k);
-    tangential_complex_->compute_tangential_complex();
-    num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
   }
 
   ~Tangential_complex_interface() {
     delete tangential_complex_;
   }
 
+  void compute_tangential_complex() {
+    tangential_complex_->compute_tangential_complex();
+    num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
+  }
+
   std::vector<double> get_point(unsigned vh) {
     std::vector<double> vd;
     if (vh < tangential_complex_->number_of_vertices()) {
@@ -104,7 +105,11 @@ class Tangential_complex_interface {
     simplex_tree->initialize_filtration();
   }
 
- private:
+  void set_max_squared_edge_length(double max_squared_edge_length) {
+    tangential_complex_->set_max_squared_edge_length(max_squared_edge_length);
+  }
+
+private:
   TC* tangential_complex_;
   TC::Num_inconsistencies num_inconsistencies_;
 };
diff --git a/src/cython/test/test_tangential_complex.py b/src/cython/test/test_tangential_complex.py
index 5385a0d3..5c62f278 100755
--- a/src/cython/test/test_tangential_complex.py
+++ b/src/cython/test/test_tangential_complex.py
@@ -32,6 +32,15 @@ def test_tangential():
     tc = TangentialComplex(intrisic_dim = 1, points=point_list)
     assert tc.__is_defined() == True
     assert tc.num_vertices() == 4
+    assert tc.num_simplices() == 0
+    assert tc.num_inconsistent_simplices() == 0
+    assert tc.num_inconsistent_stars() == 0
+
+    tc.compute_tangential_complex()
+    assert tc.num_vertices() == 4
+    assert tc.num_simplices() == 4
+    assert tc.num_inconsistent_simplices() == 0
+    assert tc.num_inconsistent_stars() == 0
 
     st = tc.create_simplex_tree()
     assert st.__is_defined() == True