Gudhi namespace. More...

Namespaces
	persistence_fields
	Field namespace.

	persistence_matrix
	Persistence matrix namespace.

Classes
class	Euclidean_distance
	Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to have the same dimension. More...

class	Lazy_toplex_map
	Lazy toplex map data structure for representing unfiltered simplicial complexes. More...

struct	Null_output_iterator

class	Off_reader
	OFF file reader top class visitor. More...

class	Points_3D_off_visitor_reader
	OFF file visitor implementation according to Off_reader in order to read points from an OFF file. More...

class	Points_3D_off_reader

class	Points_off_visitor_reader
	OFF file visitor implementation according to Off_reader in order to read points from an OFF file. More...

class	Points_off_reader
	OFF file reader implementation in order to read points from an OFF file. More...

struct	Hooks_simplex_base_dummy
	No hook when SimplexTreeOptions::link_nodes_by_label is false. More...

struct	Hooks_simplex_base_link_nodes
	Data structure to put all simplex tree nodes with same label into a list. More...

struct	linear_indexing_tag
	Tag for a linear ordering of simplices. More...

class	Simplex_tree_simplex_vertex_iterator
	Iterator over the vertices of a simplex in a SimplexTree. More...

class	Simplex_tree_boundary_simplex_iterator
	Iterator over the simplices of the boundary of a simplex. More...

class	Simplex_tree_boundary_opposite_vertex_simplex_iterator
	Iterator over the simplices of the boundary of a simplex and their opposite vertices. More...

class	Simplex_tree_complex_simplex_iterator
	Iterator over the simplices of a simplicial complex. More...

class	Simplex_tree_skeleton_simplex_iterator
	Iterator over the simplices of the skeleton of a given dimension of the simplicial complex. More...

struct	Simplex_tree_node_explicit_storage
	Node of a simplex tree with filtration value and simplex key. More...

struct	Simplex_tree_options_default

struct	Simplex_tree_options_full_featured

struct	Simplex_tree_options_minimal

class	Simplex_tree_siblings
	Data structure to store a set of nodes in a SimplexTree sharing the same parent node. More...

class	Simplex_tree_optimized_star_simplex_iterator
	Iterator over the simplices of the star of a simplex. More...

class	Simplex_tree
	Simplex Tree data structure for representing simplicial complexes. More...

class	Toplex_map
	Toplex map data structure for representing unfiltered simplicial complexes. More...

class	Persistence_interval_common

Typedefs
template<typename SimplicialComplexForProximityGraph >
using	Proximity_graph = typename boost::adjacency_list< boost::vecS, boost::vecS, boost::directedS, boost::property< vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >, boost::property< edge_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value > >
	Proximity_graph contains the vertices and edges with their filtration values in order to store the result of `Gudhi::compute_proximity_graph` function. More...

Functions
template<typename SimplicialComplexForProximityGraph , typename ForwardPointRange , typename Distance >
Proximity_graph< SimplicialComplexForProximityGraph >	compute_proximity_graph (const ForwardPointRange &points, typename SimplicialComplexForProximityGraph::Filtration_value threshold, Distance distance)
	Computes the proximity graph of the points. More...

void	read_points (std::string file_name, std::vector< std::vector< double >> &points)
	Read a set of points to turn it into a vector< vector<double> > by filling points. More...

template<typename Graph_t , typename Filtration_value , typename Vertex_handle >
Graph_t	read_graph (std::string file_name)
	Read a graph from a file. More...

template<typename Vertex_handle , typename Filtration_value >
bool	read_simplex (std::istream &in_, std::vector< Vertex_handle > &simplex, Filtration_value &fil)
	Read a face from a file. More...

template<typename Simplex_key , typename Filtration_value >
bool	read_hasse_simplex (std::istream &in_, std::vector< Simplex_key > &boundary, Filtration_value &fil)
	Read a hasse simplex from a file. More...

template<typename Filtration_value >
std::vector< std::vector< Filtration_value > >	read_lower_triangular_matrix_from_csv_file (const std::string &filename, const char separator=';')
	Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole (square) matrix. More...

template<typename OutputIterator >
void	read_persistence_intervals_and_dimension (std::string const &filename, OutputIterator out)

std::map< int, std::vector< std::pair< double, double > > >	read_persistence_intervals_grouped_by_dimension (std::string const &filename)

std::vector< std::pair< double, double > >	read_persistence_intervals_in_dimension (std::string const &filename, int only_this_dim=-1)

template<typename Persistence_interval_range >
void	write_persistence_intervals_to_stream (const Persistence_interval_range &intervals, std::ostream &out=std::cout)

Detailed Description

Gudhi namespace.

Typedef Documentation

◆ Proximity_graph

template<typename SimplicialComplexForProximityGraph >

using Gudhi::Proximity_graph = typedef typename boost::adjacency_list < boost::vecS, boost::vecS, boost::directedS , boost::property < vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value > , boost::property < edge_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value > >

Proximity_graph contains the vertices and edges with their filtration values in order to store the result of Gudhi::compute_proximity_graph function.

Template Parameters

SimplicialComplexForProximityGraph furnishes Filtration_value type definition.

Function Documentation

◆ compute_proximity_graph()

template<typename SimplicialComplexForProximityGraph , typename ForwardPointRange , typename Distance >

Proximity_graph<SimplicialComplexForProximityGraph> Gudhi::compute_proximity_graph	(	const ForwardPointRange &	points,
		typename SimplicialComplexForProximityGraph::Filtration_value	threshold,
		Distance	distance
	)

Computes the proximity graph of the points.

If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the distance function between points u and v is smaller than threshold.

Template Parameters

SimplicialComplexForProximityGraph	furnishes `Filtration_value` and `Vertex_handle` type definitions.
ForwardPointRange	furnishes `.begin()` and `.end()` methods.
Distance	furnishes `operator()(const Point& p1, const Point& p2)`, where `Point` is a point from the `ForwardPointRange`, and that returns a `Filtration_value`.

Examples: cech_complex_cgal_mini_sphere_3d.cpp.

◆ read_graph()

template<typename Graph_t , typename Filtration_value , typename Vertex_handle >

Graph_t Gudhi::read_graph ( std::string file_name )

Read a graph from a file.

Template Parameters

Graph_t	Type for the return graph. Must be constructible from iterators on pairs of Vertex_handle
Filtration_value	Type for the value of the read filtration
Vertex_handle	Type for the value of the read vertices

File format: 1 simplex per line
Dim1 X11 X12 ... X1d Fil1
Dim2 X21 X22 ... X2d Fil2
etc

The vertices must be labeled from 0 to n-1. Every simplex must appear exactly once. Simplices of dimension more than 1 are ignored.

◆ read_hasse_simplex()

template<typename Simplex_key , typename Filtration_value >

bool Gudhi::read_hasse_simplex	(	std::istream &	in_,
		std::vector< Simplex_key > &	boundary,
		Filtration_value &	fil
	)

Read a hasse simplex from a file.

File format: 1 simplex per line
Dim1 k11 k12 ... k1Dim1 Fil1
Dim2 k21 k22 ... k2Dim2 Fil2
etc

The key of a simplex is its position in the filtration order and also the number of its row in the file. Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the filtration has dimension Dimi, filtration value fil1 and simplices with key ki1 ... kiDimi in its boundary.

◆ read_lower_triangular_matrix_from_csv_file()

template<typename Filtration_value >

std::vector<std::vector<Filtration_value> > Gudhi::read_lower_triangular_matrix_from_csv_file	(	const std::string &	filename,
		const char	separator = `';'`
	)

Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole (square) matrix.

Author: Pawel Dlotko

Square matrix file format:
0;D12;...;D1j
D21;0;...;D2j
...
Dj1;Dj2;...;0

lower matrix file format:
0
D21;
D31;D32;
...
Dj1;Dj2;...;Dj(j-1);

◆ read_persistence_intervals_and_dimension()

template<typename OutputIterator >

void Gudhi::read_persistence_intervals_and_dimension	(	std::string const &	filename,
		OutputIterator	out
	)

Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death The output iterator out is used this way: *out++ = std::make_tuple(dim, birth, death); where dim is an int, birth a double, and death a double. Note: the function does not check that birth <= death.

◆ read_persistence_intervals_grouped_by_dimension()

std::map<int, std::vector<std::pair<double, double> > > Gudhi::read_persistence_intervals_grouped_by_dimension ( std::string const & filename )

inline

Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death The return value is an std::map<dim, std::vector<std::pair<birth, death>>> where dim is an int, birth a double, and death a double. Note: the function does not check that birth <= death.

◆ read_persistence_intervals_in_dimension()

std::vector<std::pair<double, double> > Gudhi::read_persistence_intervals_in_dimension	(	std::string const &	filename,
		int	only_this_dim = `-1`
	)

inline

Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death If only_this_dim = -1, dimension is ignored and all lines are returned. If only_this_dim is >= 0, only the lines where dimension = only_this_dim (or where dimension is not specified) are returned. The return value is an std::vector<std::pair<birth, death>> where dim is an int, birth a double, and death a double. Note: the function does not check that birth <= death.

Examples: bottleneck_distance.cpp.

◆ read_points()

void Gudhi::read_points	(	std::string	file_name,
		std::vector< std::vector< double >> &	points
	)

inline

Read a set of points to turn it into a vector< vector<double> > by filling points.

File format: 1 point per line
X11 X12 ... X1d
X21 X22 ... X2d
etc

◆ read_simplex()

template<typename Vertex_handle , typename Filtration_value >

bool Gudhi::read_simplex	(	std::istream &	in_,
		std::vector< Vertex_handle > &	simplex,
		Filtration_value &	fil
	)

Read a face from a file.

File format: 1 simplex per line
Dim1 X11 X12 ... X1d Fil1
Dim2 X21 X22 ... X2d Fil2
etc

The vertices must be labeled from 0 to n-1. Every simplex must appear exactly once. Simplices of dimension more than 1 are ignored.

◆ write_persistence_intervals_to_stream()

template<typename Persistence_interval_range >

void Gudhi::write_persistence_intervals_to_stream	(	const Persistence_interval_range &	intervals,
		std::ostream &	out = `std::cout`
	)

This function write a vector<Persistence_interval_common> to a stream

Namespaces

Classes

Typedefs

Functions

Detailed Description

Typedef Documentation

◆ Proximity_graph

Function Documentation

◆ compute_proximity_graph()

◆ read_graph()

◆ read_hasse_simplex()

◆ read_lower_triangular_matrix_from_csv_file()

◆ read_persistence_intervals_and_dimension()

◆ read_persistence_intervals_grouped_by_dimension()

◆ read_persistence_intervals_in_dimension()

◆ read_points()

◆ read_simplex()

◆ write_persistence_intervals_to_stream()