git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@2838 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: aa674c458f110c5c7cc3f5c987b921fcc96e3e7e

3 files changed, 150 insertions, 47 deletions

diff --git a/src/common/include/gudhi/Clock.h b/src/common/include/gudhi/Clock.h
index 77f196ca..b83de2f5 100644
--- a/src/common/include/gudhi/Clock.h
+++ b/src/common/include/gudhi/Clock.h
@@ -23,9 +23,9 @@
 #ifndef CLOCK_H_
 #define CLOCK_H_
 
-#include <boost/date_time/posix_time/posix_time.hpp>
-
+#include <iostream>
 #include <string>
+#include <chrono>
 
 namespace Gudhi {
 
@@ -33,20 +33,20 @@ class Clock {
  public:
   // Construct and start the timer
   Clock(const std::string& msg_ = std::string())
-      : startTime(boost::posix_time::microsec_clock::local_time()),
+      : startTime(std::chrono::system_clock::now()),
       end_called(false),
       msg(msg_) { }
 
   // Restart the timer
   void begin() const {
     end_called = false;
-    startTime = boost::posix_time::microsec_clock::local_time();
+    startTime = std::chrono::system_clock::now();
   }
 
   // Stop the timer
   void end() const {
     end_called = true;
-    endTime = boost::posix_time::microsec_clock::local_time();
+    endTime = std::chrono::system_clock::now();
   }
 
   std::string message() const {
@@ -62,7 +62,7 @@ class Clock {
     if (!clock.msg.empty())
       stream << clock.msg << ": ";
 
-    stream << clock.num_seconds() << "s";
+    stream << clock.num_seconds() << "s\n";
     return stream;
   }
 
@@ -71,15 +71,15 @@ class Clock {
   // - or now otherwise. In this case, the timer is not stopped.
   double num_seconds() const {
     if (!end_called) {
-      auto end = boost::posix_time::microsec_clock::local_time();
-      return (end - startTime).total_milliseconds() / 1000.;
+      auto end = std::chrono::system_clock::now();
+      return std::chrono::duration_cast<std::chrono::milliseconds>(end-startTime).count() / 1000.;
     } else {
-      return (endTime - startTime).total_milliseconds() / 1000.;
+      return std::chrono::duration_cast<std::chrono::milliseconds>(endTime-startTime).count() / 1000.;
     }
   }
 
  private:
-  mutable boost::posix_time::ptime startTime, endTime;
+  mutable std::chrono::time_point<std::chrono::system_clock> startTime, endTime;
   mutable bool end_called;
   std::string msg;
 };
diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h
index 2ec465ef..9df77760 100644
--- a/src/common/include/gudhi/random_point_generators.h
+++ b/src/common/include/gudhi/random_point_generators.h
@@ -282,6 +282,38 @@ std::vector<typename Kernel::Point_d> generate_points_on_sphere_d(std::size_t nu
 }
 
 template <typename Kernel>
+std::vector<typename Kernel::Point_d> generate_points_in_ball_d(std::size_t num_points, int dim, double radius) {
+  typedef typename Kernel::Point_d Point;
+  Kernel k;
+  CGAL::Random rng;
+  CGAL::Random_points_in_ball_d<Point> generator(dim, radius);
+  std::vector<Point> points;
+  points.reserve(num_points);
+  for (std::size_t i = 0; i < num_points;) {
+    Point p = *generator++;
+    points.push_back(p);
+    ++i;
+  }
+  return points;
+}
+
+template <typename Kernel>
+std::vector<typename Kernel::Point_d> generate_points_in_cube_d(std::size_t num_points, int dim, double radius) {
+  typedef typename Kernel::Point_d Point;
+  Kernel k;
+  CGAL::Random rng;
+  CGAL::Random_points_in_cube_d<Point> generator(dim, radius);
+  std::vector<Point> points;
+  points.reserve(num_points);
+  for (std::size_t i = 0; i < num_points;) {
+    Point p = *generator++;
+    points.push_back(p);
+    ++i;
+  }
+  return points;
+}
+
+template <typename Kernel>
 std::vector<typename Kernel::Point_d> generate_points_on_two_spheres_d(std::size_t num_points, int dim, double radius,
                                                                        double distance_between_centers,
                                                                        double radius_noise_percentage = 0.) {
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 97a87edd..90be4fc7 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -1,8 +1,8 @@
-/*    This file is part of the Gudhi Library. The Gudhi library 
- *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+/*    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):       Clement Maria, Pawel Dlotko
+ *    Author(s):       Clement Maria, Pawel Dlotko, Clement Jamin
  *
  *    Copyright (C) 2014  INRIA
  *
@@ -24,7 +24,9 @@
 #define READER_UTILS_H_
 
 #include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Debug_utils.h>
 
+#include <boost/function_output_iterator.hpp>
 #include <boost/graph/adjacency_list.hpp>
 
 #include <iostream>
@@ -34,6 +36,9 @@
 #include <string>
 #include <vector>
 #include <utility>  // for pair
+#include <tuple>  // for std::make_tuple
+
+namespace Gudhi {
 
 // Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented.
 // It is required for global functions and variables.
@@ -50,7 +55,7 @@
  * X21 X22 ... X2d<br>
  * etc<br>
  */
-inline void read_points(std::string file_name, std::vector< std::vector< double > > & points) {
+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;
@@ -60,14 +65,13 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
   std::string line;
   double x;
   while (getline(in_file, line)) {
-    std::vector< double > point;
+    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);
+    if (!point.empty()) points.push_back(point);
   }
   in_file.close();
 }
@@ -88,17 +92,20 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
  * Every simplex must appear exactly once.
  * Simplices of dimension more than 1 are ignored.
  */
-template< typename Graph_t, typename Filtration_value, typename Vertex_handle >
+template <typename Graph_t, typename Filtration_value, typename Vertex_handle>
 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::string error_str("read_graph - Unable to open file ");
+    error_str.append(file_name);
+    std::cerr << error_str << std::endl;
+    throw std::invalid_argument(error_str);
   }
 
-  typedef std::pair< Vertex_handle, Vertex_handle > Edge_t;
-  std::vector< Edge_t > edges;
-  std::vector< Filtration_value > edges_fil;
-  std::map< Vertex_handle, Filtration_value > vertices;
+  typedef std::pair<Vertex_handle, Vertex_handle> Edge_t;
+  std::vector<Edge_t> edges;
+  std::vector<Filtration_value> edges_fil;
+  std::map<Vertex_handle, Filtration_value> vertices;
 
   std::string line;
   int dim;
@@ -108,8 +115,7 @@ Graph_t read_graph(std::string file_name) {
     std::istringstream iss(line);
     while (iss >> dim) {
       switch (dim) {
-        case 0:
-        {
+        case 0: {
           iss >> u;
           iss >> fil;
           vertices[u] = fil;
@@ -118,8 +124,7 @@ Graph_t read_graph(std::string file_name) {
           }
           break;
         }
-        case 1:
-        {
+        case 1: {
           iss >> u;
           iss >> v;
           iss >> fil;
@@ -127,16 +132,13 @@ Graph_t read_graph(std::string file_name) {
           edges_fil.push_back(fil);
           break;
         }
-        default:
-        {
-          break;
-        }
+        default: { break; }
       }
     }
   }
   in_.close();
 
-  if ((size_t) (max_h + 1) != vertices.size()) {
+  if ((size_t)(max_h + 1) != vertices.size()) {
     std::cerr << "Error: vertices must be labeled from 0 to n-1 \n";
   }
 
@@ -164,8 +166,8 @@ Graph_t read_graph(std::string file_name) {
  * 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) {
+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;
@@ -189,8 +191,8 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi
  * 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) {
+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) {
@@ -209,7 +211,7 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar
 /**
  * @brief 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:<br>
@@ -226,13 +228,13 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar
  * Dj1;Dj2;...;Dj(j-1);<br>
  *
  **/
-template< typename Filtration_value >
-std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string& filename,
-                                                                                          const char separator = ';') {
+template <typename Filtration_value>
+std::vector<std::vector<Filtration_value>> read_lower_triangular_matrix_from_csv_file(const std::string& filename,
+                                                                                      const char separator = ';') {
 #ifdef DEBUG_TRACES
   std::cout << "Using procedure read_lower_triangular_matrix_from_csv_file \n";
 #endif  // DEBUG_TRACES
-  std::vector< std::vector< Filtration_value > > result;
+  std::vector<std::vector<Filtration_value>> result;
   std::ifstream in;
   in.open(filename.c_str());
   if (!in.is_open()) {
@@ -243,7 +245,7 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
 
   // the first line is emtpy, so we ignore it:
   std::getline(in, line);
-  std::vector< Filtration_value > values_in_this_line;
+  std::vector<Filtration_value> values_in_this_line;
   result.push_back(values_in_this_line);
 
   int number_of_line = 0;
@@ -251,11 +253,10 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
   // first, read the file line by line to a string:
   while (std::getline(in, line)) {
     // if line is empty, break
-    if (line.size() == 0)
-      break;
+    if (line.size() == 0) break;
 
     // if the last element of a string is comma:
-    if (line[ line.size() - 1 ] == separator) {
+    if (line[line.size() - 1] == separator) {
       // then shrink the string by one
       line.pop_back();
     }
@@ -268,7 +269,7 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
     // and now read the doubles.
 
     int number_of_entry = 0;
-    std::vector< Filtration_value > values_in_this_line;
+    std::vector<Filtration_value> values_in_this_line;
     while (iss.good()) {
       double entry;
       iss >> entry;
@@ -277,7 +278,7 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
       }
       ++number_of_entry;
     }
-    if (!values_in_this_line.empty())result.push_back(values_in_this_line);
+    if (!values_in_this_line.empty()) result.push_back(values_in_this_line);
     ++number_of_line;
   }
   in.close();
@@ -295,4 +296,74 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
   return result;
 }  // read_lower_triangular_matrix_from_csv_file
 
+/**
+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.
+**/
+template <typename OutputIterator>
+void read_persistence_intervals_and_dimension(std::string const& filename, OutputIterator out) {
+  std::ifstream in(filename);
+  if (!in.is_open()) {
+    std::string error_str("read_persistence_intervals_and_dimension - Unable to open file ");
+    error_str.append(filename);
+    std::cerr << error_str << std::endl;
+    throw std::invalid_argument(error_str);
+  }
+
+  while (!in.eof()) {
+    std::string line;
+    getline(in, line);
+    if (line.length() != 0 && line[0] != '#') {
+      double numbers[4];
+      int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
+      if (n >= 2) {
+        int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+        *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
+      }
+    }
+  }
+}
+
+/**
+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.
+**/
+inline std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(
+    std::string const& filename) {
+  std::map<int, std::vector<std::pair<double, double>>> ret;
+  read_persistence_intervals_and_dimension(
+      filename, boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) {
+        ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t)));
+      }));
+  return ret;
+}
+
+/**
+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.
+**/
+inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename,
+                                                                                      int only_this_dim = -1) {
+  std::vector<std::pair<double, double>> ret;
+  read_persistence_intervals_and_dimension(
+      filename, boost::make_function_output_iterator([only_this_dim, &ret](std::tuple<int, double, double> t) {
+        if (only_this_dim == get<0>(t) || only_this_dim == -1) ret.emplace_back(get<1>(t), get<2>(t));
+      }));
+  return ret;
+}
+
+}  // namespace Gudhi
+
 #endif  // READER_UTILS_H_