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/* This file is part of the Gudhi Library. The Gudhi library
* (Geometric Understanding in Higher Dimensions) is a generic C++
* library for computational topology.
*
* Author(s): Clément Maria
*
* Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef READER_UTILS_H_
#define READER_UTILS_H_
#include <gudhi/graph_simplicial_complex.h>
#include <boost/graph/adjacency_list.hpp>
#include <iostream>
#include <fstream>
#include <map>
#include <limits> // for numeric_limits<>
#include <string>
#include <vector>
/**
* \brief 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
*/
inline void read_points(std::string file_name, std::vector< std::vector< double > > & points) {
std::ifstream in_file(file_name.c_str(), std::ios::in);
if (!in_file.is_open()) {
std::cerr << "Unable to open file " << file_name << std::endl;
return;
}
std::string line;
double x;
while (getline(in_file, line)) {
std::vector< double > point;
std::istringstream iss(line);
while (iss >> x) {
point.push_back(x);
}
// Check for empty lines
if (!point.empty())
points.push_back(point);
}
in_file.close();
}
/**
* \brief Read a graph 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.
*/
inline Graph_t read_graph(std::string file_name) {
std::ifstream in_(file_name.c_str(), std::ios::in);
if (!in_.is_open()) {
std::cerr << "Unable to open file " << file_name << std::endl;
}
std::vector< Edge_t > edges;
std::vector< Filtration_value > edges_fil;
std::map< Vertex_handle, Filtration_value > vertices;
std::string line;
int dim;
Vertex_handle u, v, max_h = -1;
Filtration_value fil;
while (getline(in_, line)) {
std::istringstream iss(line);
while (iss >> dim) {
switch (dim) {
case 0:
{
iss >> u;
iss >> fil;
vertices[u] = fil;
if (max_h < u) {
max_h = u;
}
break;
}
case 1:
{
iss >> u;
iss >> v;
iss >> fil;
edges.push_back(Edge_t(u, v));
edges_fil.push_back(fil);
break;
}
default:
{
break;
}
}
}
}
in_.close();
if ((size_t) (max_h + 1) != vertices.size()) {
std::cerr << "Error: vertices must be labeled from 0 to n-1 \n";
}
Graph_t skel_graph(edges.begin(), edges.end(), edges_fil.begin(), vertices.size());
auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph);
boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end;
auto v_it = vertices.begin();
for (std::tie(vi, vi_end) = boost::vertices(skel_graph); vi != vi_end; ++vi, ++v_it) {
boost::put(vertex_prop, *vi, v_it->second);
}
return skel_graph;
}
/**
* \brief 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.
*/
template< typename Vertex_handle, typename Filtration_value >
bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Filtration_value & fil) {
int dim = 0;
if (!(in_ >> dim)) return false;
Vertex_handle v;
for (int i = 0; i < dim + 1; ++i) {
in_ >> v;
simplex.push_back(v);
}
in_ >> fil;
in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n'); // ignore until the carriage return
return true;
}
/**
* \brief 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.*/
template< typename Simplex_key, typename Filtration_value >
bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundary, Filtration_value & fil) {
int dim;
if (!(in_ >> dim)) return false;
if (dim == 0) {
in_ >> fil;
return true;
}
Simplex_key key;
for (int i = 0; i < dim + 1; ++i) {
in_ >> key;
boundary.push_back(key);
}
in_ >> fil;
return true;
}
#endif // READER_UTILS_H_
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