diff options
Diffstat (limited to 'src/cython/cython/witness_complex.pyx')
| -rw-r--r-- | src/cython/cython/witness_complex.pyx | 285 |
1 files changed, 22 insertions, 263 deletions
diff --git a/src/cython/cython/witness_complex.pyx b/src/cython/cython/witness_complex.pyx index b2ad4e68..e0d8b1e3 100644 --- a/src/cython/cython/witness_complex.pyx +++ b/src/cython/cython/witness_complex.pyx @@ -30,28 +30,10 @@ __license__ = "GPL v3" cdef extern from "Witness_complex_interface.h" namespace "Gudhi": cdef cppclass Witness_complex_interface "Gudhi::witness_complex::Witness_complex_interface": - Witness_complex_interface(vector[vector[double]] points, int number_of_landmarks) - 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) - 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) + Witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, + unsigned limit_dimension) # WitnessComplex python interface cdef class WitnessComplex: @@ -65,258 +47,35 @@ cdef class WitnessComplex: def __init__(self, points=None, number_of_landmarks=5): """WitnessComplex constructor. - :param points: A list of points in d-Dimension. - :type points: list of list of double - :param number_of_landmarks: Number of landmarks to build the - WitnessComplex. - :type number_of_landmarks: int + :param nearest_landmark_table: A list of nearest landmark. + :type nearest_landmark_table: list of list of pair of unsigned and double """ # The real cython constructor - def __cinit__(self, points=None, number_of_landmarks=5): - if points is not None: - self.thisptr = new Witness_complex_interface(points, - number_of_landmarks) + def __cinit__(self, nearest_landmark_table=None): + if nearest_landmark_table is not None: + self.thisptr = new Witness_complex_interface(nearest_landmark_table) def __dealloc__(self): if self.thisptr != NULL: del self.thisptr def __is_defined(self): - """Returns true if AlphaComplex pointer is not NULL. + """Returns true if WitnessComplex pointer is not NULL. """ 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. + def create_simplex_tree(self, max_alpha_square, limit_dimension = -1): """ - 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 persistence(self, homology_coeff_field=11, min_persistence=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. - """ - return self.thisptr.get_persistence(homology_coeff_field, min_persistence) - - def betti_numbers(self): - """This function returns the Betti numbers of the simplicial complex. - - :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]). - - :note: betti_numbers function requires persistence function to be - launched first. - """ - return self.thisptr.get_betti_numbers() - - def persistent_betti_numbers(self, from_value, to_value): - """This function returns the persistent Betti numbers of the - simplicial complex. - - :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: list of int -- The persistent Betti numbers ([B0, B1, ..., - Bn]). - - :note: persistent_betti_numbers function requires persistence - function to be launched first. + :param max_alpha_square: The maximum alpha square threshold the + simplices shall not exceed. Default is set to infinity. + :type max_alpha_square: float + :returns: A simplex tree created from the Delaunay Triangulation. + :rtype: SimplexTree """ - return self.thisptr.get_persistent_betti_numbers(from_value, to_value) + simplex_tree = SimplexTree() + if limit_dimension is not -1: + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square, limit_dimension) + else: + self.thisptr.create_simplex_tree(simplex_tree.thisptr, max_alpha_square) + return simplex_tree |