Cythonize Tangential

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1796 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4f9968db1b5b63f0970abcb74d4cb7a5a105b2fa

2 files changed, 62 insertions, 380 deletions

diff --git a/src/cython/cython/tangential_complex.pyx b/src/cython/cython/tangential_complex.pyx
index 01782004..35f1e384 100644
--- a/src/cython/cython/tangential_complex.pyx
+++ b/src/cython/cython/tangential_complex.pyx
@@ -3,6 +3,7 @@ from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp.string cimport string
 from libcpp cimport bool
+from cython.operator cimport dereference as deref
 import os
 
 """This file is part of the Gudhi Library. The Gudhi library
@@ -33,30 +34,15 @@ __license__ = "GPL v3"
 
 cdef extern from "Tangential_complex_interface.h" namespace "Gudhi":
     cdef cppclass Tangential_complex_interface "Gudhi::tangential_complex::Tangential_complex_interface":
-        Tangential_complex_interface(vector[vector[double]] points, double max_alpha_square)
+        Tangential_complex_interface(vector[vector[double]] points)
         # bool from_file is a workaround for cython to find the correct signature
-        Tangential_complex_interface(string off_file, double max_alpha_square, bool from_file)
-        double filtration()
-        double simplex_filtration(vector[int] simplex)
-        void set_filtration(double filtration)
-        void initialize_filtration()
-        int num_vertices()
-        int num_simplices()
-        void set_dimension(int dimension)
-        int dimension()
-        bint find_simplex(vector[int] simplex)
-        bint insert_simplex_and_subfaces(vector[int] simplex,
-                                         double filtration)
-        vector[pair[vector[int], double]] get_filtered_tree()
-        vector[pair[vector[int], double]] get_skeleton_tree(int dimension)
-        vector[pair[vector[int], double]] get_star_tree(vector[int] simplex)
-        vector[pair[vector[int], double]] get_coface_tree(vector[int] simplex,
-                                                          int dimension)
-        void remove_maximal_simplex(vector[int] simplex)
+        Tangential_complex_interface(string off_file, bool from_file)
         vector[double] get_point(int vertex)
-        vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence)
-        vector[int] get_betti_numbers()
-        vector[int] get_persistent_betti_numbers(double from_value, double to_value)
+        unsigned number_of_vertices()
+        unsigned number_of_simplices()
+        unsigned number_of_inconsistent_simplices()
+        unsigned number_of_inconsistent_stars()
+        void create_simplex_tree(Simplex_tree_interface_full_featured simplex_tree)
 
 # TangentialComplex python interface
 cdef class TangentialComplex:
@@ -81,7 +67,7 @@ cdef class TangentialComplex:
     cdef Tangential_complex_interface * thisptr
 
     # Fake constructor that does nothing but documenting the constructor
-    def __init__(self, points=None, off_file='', max_alpha_square=float('inf')):
+    def __init__(self, points=None, off_file=''):
         """TangentialComplex constructor.
 
         :param points: A list of points in d-Dimension.
@@ -91,22 +77,17 @@ cdef class TangentialComplex:
 
         :param off_file: An OFF file style name.
         :type off_file: string
-
-        :param max_alpha_square: Maximum Tangential square value. Default is :math:`\infty`
-        :type max_alpha_square: double
         """
 
     # The real cython constructor
-    def __cinit__(self, points=[], off_file='', max_alpha_square=float('inf')):
+    def __cinit__(self, points=[], off_file=''):
         if off_file is not '':
             if os.path.isfile(off_file):
-                self.thisptr = new Tangential_complex_interface(off_file,
-                    max_alpha_square, True)
+                self.thisptr = new Tangential_complex_interface(off_file, True)
             else:
                 print("file " + off_file + " not found.")
         else:
-            self.thisptr = new Tangential_complex_interface(points,
-                max_alpha_square)
+            self.thisptr = new Tangential_complex_interface(points)
                 
 
     def __dealloc__(self):
@@ -118,195 +99,6 @@ cdef class TangentialComplex:
          """
         return self.thisptr != NULL
 
-    def get_filtration(self):
-        """This function returns the main simplicial complex filtration value.
-
-        :returns:  float -- the simplicial complex filtration value.
-        """
-        return self.thisptr.filtration()
-
-    def filtration(self, simplex):
-        """This function returns the simplicial complex filtration value for a
-        given N-simplex.
-
-        :param simplex: The N-simplex, represented by a list of vertex.
-        :type simplex: list of int
-        :returns:  float -- the simplicial complex filtration value.
-        """
-        return self.thisptr.simplex_filtration(simplex)
-
-    def set_filtration(self, filtration):
-        """This function sets the main simplicial complex filtration value.
-
-        :param filtration: The filtration value.
-        :type filtration: float.
-        """
-        self.thisptr.set_filtration(<double> filtration)
-
-    def initialize_filtration(self):
-        """This function initializes and sorts the simplicial complex
-        filtration vector.
-
-        .. note::
-
-            This function must be launched before persistence, betti_numbers,
-            persistent_betti_numbers or get_filtered_tree after inserting or
-            removing simplices.
-        """
-        self.thisptr.initialize_filtration()
-
-    def num_vertices(self):
-        """This function returns the number of vertices of the simplicial
-        complex.
-
-        :returns:  int -- the simplicial complex number of vertices.
-        """
-        return self.thisptr.num_vertices()
-
-    def num_simplices(self):
-        """This function returns the number of simplices of the simplicial
-        complex.
-
-        :returns:  int -- the simplicial complex number of simplices.
-        """
-        return self.thisptr.num_simplices()
-
-    def dimension(self):
-        """This function returns the dimension of the simplicial complex.
-
-        :returns:  int -- the simplicial complex dimension.
-        """
-        return self.thisptr.dimension()
-
-    def set_dimension(self, dimension):
-        """This function sets the dimension of the simplicial complex.
-
-        :param dimension: The new dimension value.
-        :type dimension: int.
-        """
-        self.thisptr.set_dimension(<int>dimension)
-
-    def find(self, simplex):
-        """This function returns if the N-simplex was found in the simplicial
-        complex or not.
-
-        :param simplex: The N-simplex to find, represented by a list of vertex.
-        :type simplex: list of int.
-        :returns:  bool -- true if the simplex was found, false otherwise.
-        """
-        cdef vector[int] complex
-        for i in simplex:
-            complex.push_back(i)
-        return self.thisptr.find_simplex(complex)
-
-    def insert(self, simplex, filtration=0.0):
-        """This function inserts the given N-simplex with the given filtration
-        value (default value is '0.0').
-
-        :param simplex: The N-simplex to insert, represented by a list of
-            vertex.
-        :type simplex: list of int.
-        :param filtration: The filtration value of the simplex.
-        :type filtration: float.
-        :returns:  bool -- true if the simplex was found, false otherwise.
-        """
-        cdef vector[int] complex
-        for i in simplex:
-            complex.push_back(i)
-        return self.thisptr.insert_simplex_and_subfaces(complex,
-                                                        <double>filtration)
-
-    def get_filtered_tree(self):
-        """This function returns the tree sorted by increasing filtration
-        values.
-
-        :returns:  list of tuples(simplex, filtration) -- the tree sorted by
-            increasing filtration values.
-        """
-        cdef vector[pair[vector[int], double]] coface_tree \
-            = self.thisptr.get_filtered_tree()
-        ct = []
-        for filtered_complex in coface_tree:
-            v = []
-            for vertex in filtered_complex.first:
-                v.append(vertex)
-            ct.append((v, filtered_complex.second))
-        return ct
-
-    def get_skeleton_tree(self, dimension):
-        """This function returns the tree skeleton of a maximum given
-        dimension.
-
-        :param dimension: The skeleton dimension value.
-        :type dimension: int.
-        :returns:  list of tuples(simplex, filtration) -- the skeleton tree
-            of a maximum dimension.
-        """
-        cdef vector[pair[vector[int], double]] coface_tree \
-            = self.thisptr.get_skeleton_tree(<int>dimension)
-        ct = []
-        for filtered_complex in coface_tree:
-            v = []
-            for vertex in filtered_complex.first:
-                v.append(vertex)
-            ct.append((v, filtered_complex.second))
-        return ct
-
-    def get_star_tree(self, simplex):
-        """This function returns the star tree of a given N-simplex.
-
-        :param simplex: The N-simplex, represented by a list of vertex.
-        :type simplex: list of int.
-        :returns:  list of tuples(simplex, filtration) -- the star tree of a
-            simplex.
-        """
-        cdef vector[int] complex
-        for i in simplex:
-            complex.push_back(i)
-        cdef vector[pair[vector[int], double]] coface_tree \
-            = self.thisptr.get_star_tree(complex)
-        ct = []
-        for filtered_complex in coface_tree:
-            v = []
-            for vertex in filtered_complex.first:
-                v.append(vertex)
-            ct.append((v, filtered_complex.second))
-        return ct
-
-    def get_coface_tree(self, simplex, codimension):
-        """This function returns the coface tree of a given N-simplex with a
-        given codimension.
-
-        :param simplex: The N-simplex, represented by a list of vertex.
-        :type simplex: list of int.
-        :param codimension: The codimension. If codimension = 0, all cofaces
-            are returned (equivalent of get_star_tree function)
-        :type codimension: int.
-        :returns: list of tuples(simplex, filtration) -- the coface tree of a
-            simplex.
-        """
-        cdef vector[int] complex
-        for i in simplex:
-            complex.push_back(i)
-        cdef vector[pair[vector[int], double]] coface_tree \
-            = self.thisptr.get_coface_tree(complex, <int>codimension)
-        ct = []
-        for filtered_complex in coface_tree:
-            v = []
-            for vertex in filtered_complex.first:
-                v.append(vertex)
-            ct.append((v, filtered_complex.second))
-        return ct
-
-    def remove_maximal_simplex(self, simplex):
-        """This function removes a given maximal N-simplex from the simplicial
-        complex.
-
-        :param simplex: The N-simplex, represented by a list of vertex.
-        :type simplex: list of int.
-        """
-        self.thisptr.remove_maximal_simplex(simplex)
-
     def get_point(self, vertex):
         """This function returns the point corresponding to a given vertex.
 
@@ -317,47 +109,39 @@ cdef class TangentialComplex:
         cdef vector[double] point = self.thisptr.get_point(vertex)
         return point
 
-    def persistence(self, homology_coeff_field=11, min_persistence=0.0):
-        """This function returns the persistence of the simplicial complex.
-
-        :param homology_coeff_field: The homology coefficient field. Must be a
-            prime number
-        :type homology_coeff_field: int.
-        :param min_persistence: The minimum persistence value to take into
-            account (strictly greater than min_persistence). Default value is
-            0.0.
-            Sets min_persistence to -1.0 to see all values.
-        :type min_persistence: float.
-        :note: list of pairs(dimension, pair(birth, death)) -- the
-            persistence of the simplicial complex.
+    def num_vertices(self):
+        """This function returns the number of vertices.
+
+        :returns:  unsigned -- the number of vertices.
         """
-        return self.thisptr.get_persistence(homology_coeff_field, min_persistence)
+        return self.thisptr.number_of_vertices()
 
-    def betti_numbers(self):
-        """This function returns the Betti numbers of the simplicial complex.
+    def num_simplices(self):
+        """This function returns the number of simplices.
 
-        :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
+        :returns:  unsigned -- the number of simplices.
+        """
+        return self.thisptr.number_of_simplices()
 
-        :note: betti_numbers function requires persistence function to be
-            launched first.
+    def num_inconsistent_simplices(self):
+        """This function returns the number of inconsistent simplices.
+
+        :returns:  unsigned -- the number of inconsistent simplices.
         """
-        return self.thisptr.get_betti_numbers()
+        return self.thisptr.number_of_inconsistent_simplices()
 
-    def persistent_betti_numbers(self, from_value, to_value):
-        """This function returns the persistent Betti numbers of the
-        simplicial complex.
+    def num_inconsistent_stars(self):
+        """This function returns the number of inconsistent stars.
 
-        :param from_value: The persistence birth limit to be added in the
-            numbers (persistent birth <= from_value).
-        :type from_value: float.
-        :param to_value: The persistence death limit to be added in the
-            numbers (persistent death > to_value).
-        :type to_value: float.
+        :returns:  unsigned -- the number of inconsistent stars.
+        """
+        return self.thisptr.number_of_inconsistent_stars()
 
-        :returns: list of int -- The persistent Betti numbers ([B0, B1, ...,
-            Bn]).
+    def create_simplex_tree(self, SimplexTree simplex_tree):
+        """This function creates the given simplex tree from the Delaunay
+        Triangulation.
 
-        :note: persistent_betti_numbers function requires persistence
-            function to be launched first.
+        :param simplex_tree: The simplex tree to create (must be empty)
+        :type simplex_tree: SimplexTree
         """
-        return self.thisptr.get_persistent_betti_numbers(from_value, to_value)
+        self.thisptr.create_simplex_tree(deref(simplex_tree.thisptr))
\ No newline at end of file
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index e9750e85..49d66476 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -28,7 +28,6 @@
 #include <gudhi/Points_off_io.h>
 #include <CGAL/Epick_d.h>
 
-#include "Persistent_cohomology_interface.h"
 #include "Simplex_tree_interface.h"
 
 #include <vector>
@@ -50,20 +49,18 @@ class Tangential_complex_interface {
   using TC = Tangential_complex<Dynamic_kernel, CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>;
 
  public:
-  Tangential_complex_interface(std::vector<std::vector<double>>&points, double max_alpha_square)
-  : pcoh_(nullptr) {
+  Tangential_complex_interface(std::vector<std::vector<double>>&points) {
     Dynamic_kernel k;
     unsigned intrisic_dim = 0;
     if (points.size() > 0)
       intrisic_dim = points[0].size();
     
     tangential_complex_ = new TC(points, intrisic_dim, k);
-    tangential_complex_->create_complex(simplex_tree_, max_alpha_square);
-    simplex_tree_.initialize_filtration();
+    tangential_complex_->compute_tangential_complex();
+    num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
   }
 
-  Tangential_complex_interface(std::string off_file_name, double max_alpha_square, bool from_file = true)
-  : pcoh_(nullptr) {
+  Tangential_complex_interface(std::string off_file_name, bool from_file = true) {
     Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
     Dynamic_kernel k;
     unsigned intrisic_dim = 0;
@@ -72,103 +69,8 @@ class Tangential_complex_interface {
       intrisic_dim = points[0].size();
 
     tangential_complex_ = new TC(points, intrisic_dim, k);
-    tangential_complex_->create_complex(simplex_tree_, max_alpha_square);
-    simplex_tree_.initialize_filtration();
-  }
-
-  bool find_simplex(const Simplex& vh) {
-    return (simplex_tree_.find(vh) != simplex_tree_.null_simplex());
-  }
-
-  bool insert_simplex_and_subfaces(const Simplex& complex, Filtration_value filtration = 0) {
-    Insertion_result result = simplex_tree_.insert_simplex_and_subfaces(complex, filtration);
-    return (result.second);
-  }
-
-  Filtration_value simplex_filtration(const Simplex& complex) {
-    return simplex_tree_.filtration(simplex_tree_.find(complex));
-  }
-
-  void remove_maximal_simplex(const Simplex& complex) {
-    return simplex_tree_.remove_maximal_simplex(simplex_tree_.find(complex));
-  }
-
-  Complex_tree get_filtered_tree() {
-    Complex_tree filtered_tree;
-    for (auto f_simplex : simplex_tree_.filtration_simplex_range()) {
-      Simplex simplex;
-      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
-        simplex.insert(simplex.begin(), vertex);
-      }
-      filtered_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
-    }
-    return filtered_tree;
-
-  }
-
-  Complex_tree get_skeleton_tree(int dimension) {
-    Complex_tree skeleton_tree;
-    for (auto f_simplex : simplex_tree_.skeleton_simplex_range(dimension)) {
-      Simplex simplex;
-      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
-        simplex.insert(simplex.begin(), vertex);
-      }
-      skeleton_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
-    }
-    return skeleton_tree;
-  }
-
-  Complex_tree get_star_tree(const Simplex& complex) {
-    Complex_tree star_tree;
-    for (auto f_simplex : simplex_tree_.star_simplex_range(simplex_tree_.find(complex))) {
-      Simplex simplex;
-      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
-        simplex.insert(simplex.begin(), vertex);
-      }
-      star_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
-    }
-    return star_tree;
-  }
-
-  Complex_tree get_coface_tree(const Simplex& complex, int dimension) {
-    Complex_tree coface_tree;
-    for (auto f_simplex : simplex_tree_.cofaces_simplex_range(simplex_tree_.find(complex), dimension)) {
-      Simplex simplex;
-      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
-        simplex.insert(simplex.begin(), vertex);
-      }
-      coface_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
-    }
-    return coface_tree;
-  }
-
-  // Specific to Witness complex because no inheritance
-  Filtration_value filtration() const {
-    return simplex_tree_.filtration();
-  }
-
-  void set_filtration(Filtration_value fil) {
-    simplex_tree_.set_filtration(fil);
-  }
-
-  void initialize_filtration() {
-    simplex_tree_.initialize_filtration();
-  }
-
-  size_t num_vertices() const {
-    return simplex_tree_.num_vertices();
-  }
-
-  size_t num_simplices() {
-    return simplex_tree_.num_simplices();
-  }
-
-  int dimension() const {
-    return simplex_tree_.dimension();
-  }
-
-  void set_dimension(int dimension) {
-    simplex_tree_.set_dimension(dimension);
+    tangential_complex_->compute_tangential_complex();
+    num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
   }
 
   std::vector<double> get_point(int vh) {
@@ -183,34 +85,30 @@ class Tangential_complex_interface {
     return vd;
   }
 
-  std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field, double min_persistence) {
-    if (pcoh_ != nullptr) {
-      delete pcoh_;
-    }
-    pcoh_ = new Persistent_cohomology_interface<Simplex_tree<>>(&simplex_tree_);
-    return pcoh_->get_persistence(homology_coeff_field, min_persistence);
+  unsigned number_of_vertices() {
+    return tangential_complex_->number_of_vertices();
   }
-  
-  std::vector<int> get_betti_numbers() const {
-    if (pcoh_ != nullptr) {
-      return pcoh_->betti_numbers();
-    }
-    std::vector<int> betti_numbers;
-    return betti_numbers;
+
+  unsigned number_of_simplices() {
+    return num_inconsistencies_.num_simplices;
   }
 
-  std::vector<int> get_persistent_betti_numbers(Filtration_value from, Filtration_value to) const {
-    if (pcoh_ != nullptr) {
-      return pcoh_->persistent_betti_numbers(from, to);
-    }
-    std::vector<int> persistent_betti_numbers;
-    return persistent_betti_numbers;
+  unsigned number_of_inconsistent_simplices() {
+    return num_inconsistencies_.num_inconsistent_simplices;
   }
-  
+
+  unsigned number_of_inconsistent_stars() {
+    return num_inconsistencies_.num_inconsistent_stars;
+  }
+
+  void create_simplex_tree(Simplex_tree<>& simplex_tree) {
+    tangential_complex_->create_complex<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>(simplex_tree);
+    simplex_tree.initialize_filtration();
+  }
+
  private:
-  Simplex_tree<> simplex_tree_;
-  Persistent_cohomology_interface<Simplex_tree<>>* pcoh_;
   TC* tangential_complex_;
+  TC::Num_inconsistencies num_inconsistencies_;
 };
 
 }  // namespace tangential_complex