Merge C++ version of persistence representation

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration_bis@3043 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 6421c7cbe670fad1a8900ccc0ea6ff32297dd5e7

7 files changed, 387 insertions, 0 deletions

diff --git a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt
new file mode 100644
index 00000000..e3d1013b
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt
@@ -0,0 +1,38 @@
+cmake_minimum_required(VERSION 2.6)
+project(Persistence_vectors_utilities)
+
+file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
+
+add_executable ( create_persistence_vectors create_persistence_vectors.cpp )
+target_link_libraries(create_persistence_vectors ${Boost_SYSTEM_LIBRARY})
+
+# Will create simple_diagram.txt.vect
+add_test(NAME create_persistence_vectors COMMAND $<TARGET_FILE:create_persistence_vectors>
+    "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt")
+
+add_executable ( average_persistence_vectors average_persistence_vectors.cpp )
+target_link_libraries(average_persistence_vectors ${Boost_SYSTEM_LIBRARY})
+
+add_test(NAME average_persistence_vectors COMMAND $<TARGET_FILE:average_persistence_vectors>
+    "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect"
+    "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect")
+
+add_executable ( compute_distance_of_persistence_vectors compute_distance_of_persistence_vectors.cpp )
+target_link_libraries(compute_distance_of_persistence_vectors ${Boost_SYSTEM_LIBRARY})
+
+add_test(NAME compute_distance_of_persistence_vectors COMMAND $<TARGET_FILE:compute_distance_of_persistence_vectors>
+    "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect"
+    "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect")
+
+add_executable ( compute_scalar_product_of_persistence_vectors compute_scalar_product_of_persistence_vectors.cpp )
+target_link_libraries(compute_scalar_product_of_persistence_vectors ${Boost_SYSTEM_LIBRARY})
+
+add_test(NAME compute_scalar_product_of_persistence_vectors COMMAND $<TARGET_FILE:compute_scalar_product_of_persistence_vectors>
+    "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect"
+    "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect")
+
+add_executable ( plot_persistence_vectors plot_persistence_vectors.cpp )
+target_link_libraries(plot_persistence_vectors ${Boost_SYSTEM_LIBRARY})
+
+add_test(NAME plot_persistence_vectors COMMAND $<TARGET_FILE:plot_persistence_vectors>
+    "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt.vect")
diff --git a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp
new file mode 100644
index 00000000..366ee2bc
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp
@@ -0,0 +1,67 @@
+/*    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_vectors.h>
+
+#include <iostream>
+#include <vector>
+
+using Euclidean_distance = Gudhi::Euclidean_distance;
+using Vector_distances_in_diagram =
+  Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program computes average persistence vector of persistence vectors created based on persistence "
+               "diagrams provided as an input. \n";
+  std::cout << "Please call this program with the names of files with persistence diagrams \n";
+  std::vector<const char*> filenames;
+
+  if (argc == 1) {
+    std::cout << "No input files given, the program will now terminate \n";
+    return 1;
+  }
+
+  for (int i = 1; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+
+  std::cout << "Reading persistence vectors...\n";
+  std::vector<Vector_distances_in_diagram*> lands;
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    Vector_distances_in_diagram* l = new Vector_distances_in_diagram;
+    l->load_from_file(filenames[i]);
+    lands.push_back(l);
+  }
+
+  Vector_distances_in_diagram av;
+  av.compute_average(lands);
+
+  av.print_to_file("average.vect");
+
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    delete lands[i];
+  }
+
+  std::cout << "Done \n";
+
+  return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp
new file mode 100644
index 00000000..3aed297e
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.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_vectors.h>
+
+#include <iostream>
+#include <sstream>
+#include <limits>
+#include <vector>
+
+using Euclidean_distance = Gudhi::Euclidean_distance;
+using Vector_distances_in_diagram =
+  Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program compute distance of persistence vectors stored in a file (the file needs to be created "
+               "beforehand). \n";
+  std::cout << "The first parameter of a program is an integer p. The program compute l^p distance of the vectors. For "
+               "l^infty distance choose p = -1. \n";
+  std::cout << "The remaining parameters of this programs are names of files with persistence vectors.\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<Vector_distances_in_diagram> vectors;
+  vectors.reserve(filenames.size());
+  for (size_t file_no = 0; file_no != filenames.size(); ++file_no) {
+    Vector_distances_in_diagram l;
+    l.load_from_file(filenames[file_no]);
+    vectors.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 != vectors.size(); ++i) {
+    for (size_t j = i + 1; j != vectors.size(); ++j) {
+      distance[i][j] = distance[j][i] = vectors[i].distance(vectors[j], p);
+    }
+  }
+
+  // and now output the result to the screen and a file:
+  std::ofstream out;
+  out.open("distance");
+  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();
+
+  return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
new file mode 100644
index 00000000..d9ad4360
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
@@ -0,0 +1,80 @@
+/*    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_vectors.h>
+
+#include <iostream>
+#include <sstream>
+#include <limits>
+#include <vector>
+
+using Euclidean_distance = Gudhi::Euclidean_distance;
+using Vector_distances_in_diagram =
+  Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program compute scalar product of persistence vectors stored in a file (the file needs to be "
+               "created beforehand). \n";
+  std::cout << "The parameters of this programs are names of files with persistence vectors.\n";
+
+  std::vector<const char*> filenames;
+  for (int i = 1; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+  std::vector<Vector_distances_in_diagram> vectors;
+  vectors.reserve(filenames.size());
+  for (size_t file_no = 0; file_no != filenames.size(); ++file_no) {
+    Vector_distances_in_diagram l;
+    l.load_from_file(filenames[file_no]);
+    vectors.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 != vectors.size(); ++i) {
+    for (size_t j = i; j != vectors.size(); ++j) {
+      scalar_product[i][j] = scalar_product[j][i] = vectors[i].compute_scalar_product(vectors[j]);
+    }
+  }
+
+  // and now output the result to the screen and a file:
+  std::ofstream out;
+  out.open("scalar_product");
+  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();
+  return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp
new file mode 100644
index 00000000..b618ca67
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.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_vectors.h>
+
+#include <iostream>
+#include <sstream>
+#include <limits>
+#include <vector>
+
+using Euclidean_distance = Gudhi::Euclidean_distance;
+using Vector_distances_in_diagram =
+  Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program creates persistence vectors of diagrams provided as an input. The first parameter of this "
+               "program is a dimension of persistence ";
+  std::cout << " that will be used in creation of the persistence vectors. If our input files contain persistence "
+               "pairs of various dimension, as a second parameter of the ";
+  std::cout << " procedure please provide the dimension of persistence you want to use. If in your file there are only "
+               "birth-death pairs of the same dimension, set the first parameter to -1."
+            << std::endl;
+  std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
+  int dim = atoi(argv[1]);
+  unsigned dimension = std::numeric_limits<unsigned>::max();
+  if (dim >= 0) {
+    dimension = (unsigned)dim;
+  }
+
+  std::vector<const char*> filenames;
+  for (int i = 2; i < argc; ++i) {
+    filenames.push_back(argv[i]);
+  }
+
+  for (size_t i = 0; i != filenames.size(); ++i) {
+    std::cerr << "Creating persistence vectors based on a file : " << filenames[i] << std::endl;
+    Vector_distances_in_diagram l(filenames[i], dimension);
+    std::stringstream ss;
+    ss << filenames[i] << ".vect";
+    l.print_to_file(ss.str().c_str());
+  }
+  std::cout << "Done \n";
+  return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp
new file mode 100644
index 00000000..e52b8f7d
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp
@@ -0,0 +1,44 @@
+/*    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_vectors.h>
+
+#include <iostream>
+#include <sstream>
+
+using Euclidean_distance = Gudhi::Euclidean_distance;
+using Vector_distances_in_diagram =
+  Gudhi::Persistence_representations::Vector_distances_in_diagram<Euclidean_distance>;
+
+int main(int argc, char** argv) {
+  std::cout << "This program create a Gnuplot script to plot persistence vector. Please call this program with the "
+               "name of file with persistence vector. \n";
+  if (argc != 2) {
+    std::cout << "Wrong number of parameters, the program will now terminate. \n";
+    return 1;
+  }
+  Vector_distances_in_diagram l;
+  l.load_from_file(argv[1]);
+  l.plot(argv[1]);
+
+  return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect b/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect
new file mode 100644
index 00000000..1d4eeaaf
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect
@@ -0,0 +1 @@
+0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 
\ No newline at end of file