GUDHI 2.1.0 as released by upstream in a tarball.upstream/2.1.0

10 files changed, 701 insertions, 0 deletions

diff --git a/utilities/Persistence_representations/persistence_heat_maps/CMakeLists.txt b/utilities/Persistence_representations/persistence_heat_maps/CMakeLists.txt
new file mode 100644
index 00000000..386e9fa5
--- /dev/null
+++ b/utilities/Persistence_representations/persistence_heat_maps/CMakeLists.txt
@@ -0,0 +1,15 @@
+cmake_minimum_required(VERSION 2.6)
+project(Persistence_representations_heat_maps_utilities)
+
+add_persistence_representation_creation_utility(create_pssk  "10" "-1" "-1" "4" "-1")
+add_persistence_representation_creation_utility(create_p_h_m_weighted_by_arctan_of_their_persistence "10" "-1" "-1" "4" "-1")
+add_persistence_representation_creation_utility(create_p_h_m_weighted_by_distance_from_diagonal "10" "-1" "-1" "4" "-1")
+add_persistence_representation_creation_utility(create_p_h_m_weighted_by_squared_diag_distance "10" "-1" "-1" "4" "-1")
+# Need to set grid min and max for further average, distance and scalar_product
+add_persistence_representation_creation_utility(create_persistence_heat_maps "10" "0" "35" "10" "-1")
+
+add_persistence_representation_plot_utility(plot_persistence_heat_map ".mps")
+
+add_persistence_representation_function_utility(average_persistence_heat_maps ".mps")
+add_persistence_representation_function_utility(compute_distance_of_persistence_heat_maps ".mps" "1")
+add_persistence_representation_function_utility(compute_scalar_product_of_persistence_heat_maps ".mps")
diff --git a/utilities/Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp b/utilities/Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp
new file mode 100644
index 00000000..6739e0b6
--- /dev/null
+++ b/utilities/Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp
@@ -0,0 +1,63 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2016  INRIA (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/>.
+ */
+
+#include <gudhi/Persistence_heat_maps.h>
+
+#include <iostream>
+#include <vector>
+
+using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program computes average of persistence heat maps stored in files (the files needs to be "
+            << "created beforehand).\n"
+            << "The parameters of this programs are names of files with persistence heat maps.\n";
+
+  if (argc < 3) {
+    std::cout << "Wrong number of parameters, the program will now terminate \n";
+    return 1;
+  }
+
+  std::vector<const char*> filenames;
+  for (int i = 1; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+
+  std::vector<Persistence_heat_maps*> maps;
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    Persistence_heat_maps* l = new Persistence_heat_maps;
+    l->load_from_file(filenames[i]);
+    maps.push_back(l);
+  }
+
+  Persistence_heat_maps av;
+  av.compute_average(maps);
+  av.print_to_file("average.mps");
+
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    delete maps[i];
+  }
+
+  std::cout << "Average can be found in 'average.mps' file\n";
+  return 0;
+}
diff --git a/utilities/Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/utilities/Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
new file mode 100644
index 00000000..ed8278a2
--- /dev/null
+++ b/utilities/Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
@@ -0,0 +1,94 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2016  INRIA (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/>.
+ */
+
+#include <gudhi/Persistence_heat_maps.h>
+
+#include <iostream>
+#include <sstream>
+#include <limits>
+#include <vector>
+
+using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program computes distance of persistence heat maps stored in files (the files needs to be "
+            << "created beforehand).\n"
+            << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat "
+            << "maps. For L^infty distance choose p = -1. \n"
+            << "The remaining parameters of this program are names of files with persistence heat maps.\n";
+
+  if (argc < 3) {
+    std::cout << "Wrong number of parameters, the program will now terminate \n";
+    return 1;
+  }
+
+  int pp = atoi(argv[1]);
+  double p = std::numeric_limits<double>::max();
+  if (pp != -1) {
+    p = pp;
+  }
+
+  std::vector<const char*> filenames;
+  for (int i = 2; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+  std::vector<Persistence_heat_maps> maps;
+  maps.reserve(filenames.size());
+  for (size_t file_no = 0; file_no != filenames.size(); ++file_no) {
+    Persistence_heat_maps l;
+    l.load_from_file(filenames[file_no]);
+    maps.push_back(l);
+  }
+
+  // and now we will compute the scalar product of landscapes.
+
+  // first we prepare an array:
+  std::vector<std::vector<double> > distance(filenames.size());
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::vector<double> v(filenames.size(), 0);
+    distance[i] = v;
+  }
+
+  // and now we can compute the distances:
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    for (size_t j = i; j != filenames.size(); ++j) {
+      distance[i][j] = distance[j][i] = maps[i].distance(maps[j], p);
+    }
+  }
+
+  // and now output the result to the screen and a file:
+  std::ofstream out;
+  out.open("distance.mps");
+  for (size_t i = 0; i != distance.size(); ++i) {
+    for (size_t j = 0; j != distance.size(); ++j) {
+      std::cout << distance[i][j] << " ";
+      out << distance[i][j] << " ";
+    }
+    std::cout << std::endl;
+    out << std::endl;
+  }
+  out.close();
+
+  std::cout << "Distance can be found in 'distance.mps' file\n";
+  return 0;
+}
diff --git a/utilities/Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/utilities/Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
new file mode 100644
index 00000000..63626853
--- /dev/null
+++ b/utilities/Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
@@ -0,0 +1,85 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2016  INRIA (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/>.
+ */
+
+#include <gudhi/Persistence_heat_maps.h>
+
+#include <iostream>
+#include <sstream>
+#include <vector>
+
+using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program computes scalar product of persistence heat maps stored in a file (the file needs to be "
+            << "created beforehand). \n"
+            << "The parameters of this programs are names of files with persistence heat maps.\n";
+
+  if (argc < 3) {
+    std::cout << "Wrong number of parameters, the program will now terminate \n";
+    return 1;
+  }
+
+  std::vector<const char*> filenames;
+  for (int i = 1; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+  std::vector<Persistence_heat_maps> maps;
+  maps.reserve(filenames.size());
+  for (size_t file_no = 0; file_no != filenames.size(); ++file_no) {
+    Persistence_heat_maps l;
+    l.load_from_file(filenames[file_no]);
+    maps.push_back(l);
+  }
+
+  // and now we will compute the scalar product of landscapes.
+
+  // first we prepare an array:
+  std::vector<std::vector<double> > scalar_product(filenames.size());
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::vector<double> v(filenames.size(), 0);
+    scalar_product[i] = v;
+  }
+
+  // and now we can compute the scalar product:
+  for (size_t i = 0; i != maps.size(); ++i) {
+    for (size_t j = i; j != maps.size(); ++j) {
+      scalar_product[i][j] = scalar_product[j][i] = maps[i].compute_scalar_product(maps[j]);
+    }
+  }
+
+  // and now output the result to the screen and a file:
+  std::ofstream out;
+  out.open("scalar_product.mps");
+  for (size_t i = 0; i != scalar_product.size(); ++i) {
+    for (size_t j = 0; j != scalar_product.size(); ++j) {
+      std::cout << scalar_product[i][j] << " ";
+      out << scalar_product[i][j] << " ";
+    }
+    std::cout << std::endl;
+    out << std::endl;
+  }
+  out.close();
+
+  std::cout << "Distance can be found in 'scalar_product.mps' file\n";
+  return 0;
+}
diff --git a/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
new file mode 100644
index 00000000..b4a1daa5
--- /dev/null
+++ b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
@@ -0,0 +1,81 @@
+/*    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):       Pawel Dlotko
+*
+*    Copyright (C) 2016  INRIA (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/>.
+*/
+
+#include <gudhi/Persistence_heat_maps.h>
+
+#include <iostream>
+#include <sstream>
+#include <limits>
+#include <vector>
+
+using arc_tan_of_persistence_of_point = Gudhi::Persistence_representations::arc_tan_of_persistence_of_point;
+using Persistence_heat_maps =
+    Gudhi::Persistence_representations::Persistence_heat_maps<arc_tan_of_persistence_of_point>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) "
+            << "provided as an input.The Gaussian kernels are weighted by the arc tangential of their persistence.\n"
+            << "The first parameter of a program is an integer, a size of a grid.\n"
+            << "The second and third parameters are min and max of the grid. If you want those numbers to be computed "
+            << "based on the data, set them both to -1 \n"
+            << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number "
+            << "of pixels.\n"
+            << "The fifth parameter of this program is a dimension of persistence that will be used in creation of "
+            << "the persistence heat maps."
+            << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the "
+            << "procedure please provide the dimension of persistence you want to use."
+            << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to "
+            << "-1.\n"
+            << "The remaining parameters are the names of files with persistence diagrams. \n";
+
+  if (argc < 7) {
+    std::cout << "Wrong parameter list, the program will now terminate \n";
+    return 1;
+  }
+
+  size_t size_of_grid = (size_t)atoi(argv[1]);
+  double min_ = atof(argv[2]);
+  double max_ = atof(argv[3]);
+  size_t stdiv = atof(argv[4]);
+
+  unsigned dimension = std::numeric_limits<unsigned>::max();
+  int dim = atoi(argv[5]);
+  if (dim >= 0) {
+    dimension = (unsigned)dim;
+  }
+
+  std::vector<const char*> filenames;
+  for (int i = 6; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+
+  std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1);
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
+    Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension);
+
+    std::stringstream ss;
+    ss << filenames[i] << ".mps";
+    l.print_to_file(ss.str().c_str());
+  }
+  return 0;
+}
diff --git a/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
new file mode 100644
index 00000000..c50f9ddb
--- /dev/null
+++ b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
@@ -0,0 +1,81 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2016  INRIA (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/>.
+ */
+
+#include <gudhi/Persistence_heat_maps.h>
+
+#include <iostream>
+#include <sstream>
+#include <limits>
+#include <vector>
+
+using distance_from_diagonal_scaling = Gudhi::Persistence_representations::distance_from_diagonal_scaling;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<distance_from_diagonal_scaling>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) "
+            << "provided as an input.The Gaussian kernels are weighted by the distance of a center from the "
+            << "diagonal.\n"
+            << "The first parameter of a program is an integer, a size of a grid.\n"
+            << "The second and third parameters are min and max of the grid. If you want those numbers to be computed "
+            << "based on the data, set them both to -1 \n"
+            << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number "
+            << "of pixels.\n"
+            << "The fifth parameter of this program is a dimension of persistence that will be used in creation of "
+            << "the persistence heat maps."
+            << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the "
+            << "procedure please provide the dimension of persistence you want to use."
+            << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to "
+            << "-1.\n"
+            << "The remaining parameters are the names of files with persistence diagrams. \n";
+
+  if (argc < 7) {
+    std::cout << "Wrong parameter list, the program will now terminate \n";
+    return 1;
+  }
+
+  size_t size_of_grid = (size_t)atoi(argv[1]);
+  double min_ = atof(argv[2]);
+  double max_ = atof(argv[3]);
+  size_t stdiv = atof(argv[4]);
+
+  unsigned dimension = std::numeric_limits<unsigned>::max();
+  int dim = atoi(argv[5]);
+  if (dim >= 0) {
+    dimension = (unsigned)dim;
+  }
+
+  std::vector<const char*> filenames;
+  for (int i = 6; i != argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+
+  std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1);
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
+    Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension);
+
+    std::stringstream ss;
+    ss << filenames[i] << ".mps";
+    l.print_to_file(ss.str().c_str());
+  }
+  return 0;
+}
diff --git a/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
new file mode 100644
index 00000000..59ff3c24
--- /dev/null
+++ b/utilities/Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
@@ -0,0 +1,83 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2016  INRIA (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/>.
+ */
+
+#include <gudhi/Persistence_heat_maps.h>
+
+#include <iostream>
+#include <sstream>
+#include <limits>
+#include <vector>
+
+using squared_distance_from_diagonal_scaling =
+    Gudhi::Persistence_representations::squared_distance_from_diagonal_scaling;
+using Persistence_heat_maps =
+    Gudhi::Persistence_representations::Persistence_heat_maps<squared_distance_from_diagonal_scaling>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) "
+            << "provided as an input.The Gaussian kernels are weighted by the square of distance of a center from the "
+            << "diagonal.\n"
+            << "The first parameter of a program is an integer, a size of a grid.\n"
+            << "The second and third parameters are min and max of the grid. If you want those numbers to be computed "
+            << "based on the data, set them both to -1 \n"
+            << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number "
+            << "of pixels.\n"
+            << "The fifth parameter of this program is a dimension of persistence that will be used in creation of "
+            << "the persistence heat maps."
+            << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the "
+            << "procedure please provide the dimension of persistence you want to use."
+            << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to "
+            << "-1.\n"
+            << "The remaining parameters are the names of files with persistence diagrams. \n";
+
+  if (argc < 7) {
+    std::cout << "Wrong parameter list, the program will now terminate \n";
+    return 1;
+  }
+
+  size_t size_of_grid = (size_t)atoi(argv[1]);
+  double min_ = atof(argv[2]);
+  double max_ = atof(argv[3]);
+  size_t stdiv = atof(argv[4]);
+
+  unsigned dimension = std::numeric_limits<unsigned>::max();
+  int dim = atoi(argv[5]);
+  if (dim >= 0) {
+    dimension = (unsigned)dim;
+  }
+
+  std::vector<const char*> filenames;
+  for (int i = 6; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+
+  std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1);
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl;
+    Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension);
+
+    std::stringstream ss;
+    ss << filenames[i] << ".mps";
+    l.print_to_file(ss.str().c_str());
+  }
+  return 0;
+}
diff --git a/utilities/Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp b/utilities/Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp
new file mode 100644
index 00000000..25cd1067
--- /dev/null
+++ b/utilities/Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp
@@ -0,0 +1,78 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2016  INRIA (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/>.
+ */
+
+#include <gudhi/Persistence_heat_maps.h>
+
+#include <iostream>
+#include <sstream>
+#include <limits>
+#include <vector>
+
+using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program creates persistence heat map files (*.mps) of persistence diagrams files (*.pers) "
+            << "provided as an input.\n"
+            << "The first parameter of a program is an integer, a size of a grid.\n"
+            << "The second and third parameters are min and max of the grid. If you want those numbers to be computed "
+            << "based on the data, set them both to -1 \n"
+            << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number "
+            << "of pixels.\n"
+            << "The fifth parameter of this program is a dimension of persistence that will be used in creation of "
+            << "the persistence heat maps."
+            << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the "
+            << "procedure please provide the dimension of persistence you want to use."
+            << "If in your files there are only birth-death pairs of the same dimension, set the fifth parameter to "
+            << "-1.\n"
+            << "The remaining parameters are the names of files with persistence diagrams. \n";
+
+  if (argc < 7) {
+    std::cout << "Wrong parameter list, the program will now terminate \n";
+    return 1;
+  }
+  size_t size_of_grid = (size_t)atoi(argv[1]);
+  double min_ = atof(argv[2]);
+  double max_ = atof(argv[3]);
+  size_t stdiv = atof(argv[4]);
+
+  unsigned dimension = std::numeric_limits<unsigned>::max();
+  int dim = atoi(argv[5]);
+  if (dim >= 0) {
+    dimension = (unsigned)dim;
+  }
+  std::vector<const char*> filenames;
+  for (int i = 6; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+
+  std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1);
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::cout << "Creating a heat map based on file : " << filenames[i] << std::endl;
+    Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension);
+
+    std::stringstream ss;
+    ss << filenames[i] << ".mps";
+    l.print_to_file(ss.str().c_str());
+  }
+  return 0;
+}
diff --git a/utilities/Persistence_representations/persistence_heat_maps/create_pssk.cpp b/utilities/Persistence_representations/persistence_heat_maps/create_pssk.cpp
new file mode 100644
index 00000000..97ddb8f0
--- /dev/null
+++ b/utilities/Persistence_representations/persistence_heat_maps/create_pssk.cpp
@@ -0,0 +1,79 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2016  INRIA (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/>.
+ */
+
+#include <gudhi/PSSK.h>
+
+#include <iostream>
+#include <sstream>
+#include <limits>
+#include <vector>
+
+using PSSK = Gudhi::Persistence_representations::PSSK;
+
+int main(int argc, char** argv) {
+  std::cout << "This program creates PSSK files (*.pssk) of persistence diagrams files (*.pers) "
+            << "provided as an input.\n"
+            << "The first parameter of a program is an integer, a size of a grid.\n"
+            << "The second and third parameters are min and max of the grid. If you want those numbers to be computed "
+            << "based on the data, set them both to -1 \n"
+            << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number "
+            << "of pixels.\n"
+            << "The fifth parameter of this program is a dimension of persistence that will be used in creation of "
+            << "the PSSK."
+            << "If your input files contains persistence pairs of various dimension, as a fifth parameter of the "
+            << "procedure please provide the dimension of persistence you want to use."
+            << "If in your files there are only birth-death pairs of the same dimension, set the first parameter to "
+            << "-1.\n"
+            << "The remaining parameters are the names of files with persistence diagrams. \n";
+
+  if (argc < 7) {
+    std::cout << "Wrong parameter list, the program will now terminate \n";
+    return 1;
+  }
+
+  size_t size_of_grid = (size_t)atoi(argv[1]);
+  double min_ = atof(argv[2]);
+  double max_ = atof(argv[3]);
+  size_t stdiv = atof(argv[4]);
+
+  unsigned dimension = std::numeric_limits<unsigned>::max();
+  int dim = atoi(argv[5]);
+  if (dim >= 0) {
+    dimension = (unsigned)dim;
+  }
+
+  std::vector<const char*> filenames;
+  for (int i = 6; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+
+  std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1);
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::cout << "Creating a PSSK based on a file : " << filenames[i] << std::endl;
+    PSSK l(filenames[i], filter, size_of_grid, min_, max_, dimension);
+
+    std::stringstream ss;
+    ss << filenames[i] << ".pssk";
+    l.print_to_file(ss.str().c_str());
+  }
+  return 0;
+}
diff --git a/utilities/Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp b/utilities/Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp
new file mode 100644
index 00000000..63711d83
--- /dev/null
+++ b/utilities/Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp
@@ -0,0 +1,42 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2016  INRIA (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/>.
+ */
+
+#include <gudhi/Persistence_heat_maps.h>
+
+#include <iostream>
+#include <sstream>
+
+using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function;
+using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program creates a gnuplot script from a persistence heat maps stored in a file (the file needs "
+            << "to be created beforehand). Please call the code with the name of a single heat maps file \n";
+  if (argc != 2) {
+    std::cout << "Wrong parameter list, the program will now terminate \n";
+    return 1;
+  }
+  Persistence_heat_maps l;
+  l.load_from_file(argv[1]);
+  l.plot(argv[1]);
+  return 0;
+}