cpplint fixes

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/VR_witness@984 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c663c383e09719a8c70c1100bb6e21d8fc49e597

4 files changed, 403 insertions, 0 deletions

diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
new file mode 100644
index 00000000..b304479e
--- /dev/null
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -0,0 +1,44 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHIWitnessComplex)
+
+# A simple example
+   add_executable( witness_complex_from_file witness_complex_from_file.cpp )
+   add_test( witness_complex_from_bunny ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100)   
+
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+    message(STATUS "CGAL version: ${CGAL_VERSION}.")
+
+    include( ${CGAL_USE_FILE} )
+    # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
+    # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+    # A workaround is to add "-std=c++11" again.
+    # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
+    # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
+    # but it implies to use cmake version 3.1 at least.
+    if(NOT MSVC)
+      include(CheckCXXCompilerFlag)
+      CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
+      if(COMPILER_SUPPORTS_CXX11)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+      endif()
+    endif()
+    # - End of workaround
+
+    find_package(Eigen3 3.1.0)
+    if (EIGEN3_FOUND)
+      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+      include( ${EIGEN3_USE_FILE} )
+      message(STATUS "Eigen3 use file: ${EIGEN3_USE_FILE}.")
+      include_directories (BEFORE "../../include")
+
+      add_executable ( witness_complex_sphere witness_complex_sphere.cpp )
+      target_link_libraries(witness_complex_sphere ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_test( witness_complex_sphere_10 ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_sphere 10)   
+    else()
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for witness_complex_sphere example.")      
+    endif()
+  else()
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile witness_complex_sphere example. Version 4.6.0 is required.")
+  endif ()
+endif()
diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h
new file mode 100644
index 00000000..ac445261
--- /dev/null
+++ b/src/Witness_complex/example/generators.h
@@ -0,0 +1,147 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2015  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 EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
+#define EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
+
+#include <CGAL/Epick_d.h>
+#include <CGAL/point_generators_d.h>
+
+#include <fstream>
+#include <string>
+#include <vector>
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef K::FT FT;
+typedef K::Point_d Point_d;
+typedef std::vector<Point_d> Point_Vector;
+typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator;
+typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
+
+/**
+ * \brief Rock age method of reading off file
+ *
+ */
+inline void
+off_reader_cust(std::string file_name, std::vector<Point_d> & 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;
+  // Line OFF. No need in it
+  if (!getline(in_file, line)) {
+    std::cerr << "No line OFF\n";
+    return;
+  }
+  // Line with 3 numbers. No need
+  if (!getline(in_file, line)) {
+    std::cerr << "No line with 3 numbers\n";
+    return;
+  }
+  // Reading points
+  while (getline(in_file, line)) {
+    std::vector< double > point;
+    std::istringstream iss(line);
+    while (iss >> x) {
+      point.push_back(x);
+    }
+    points.push_back(Point_d(point));
+  }
+  in_file.close();
+}
+
+/**
+ * \brief Customized version of read_points
+ * which takes into account a possible nbP first line
+ *
+ */
+inline void
+read_points_cust(std::string file_name, Point_Vector & 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);
+    }
+    Point_d p(point.begin(), point.end());
+    if (point.size() != 1)
+      points.push_back(p);
+  }
+  in_file.close();
+}
+
+/** \brief Generate points on a grid in a cube of side 2
+ * having {+-1}^D as vertices and insert them in W.
+ * The grid has "width" points on each side. 
+ * If torus is true then it is supposed that the cube represents
+ * a flat torus, hence the opposite borders are associated.
+ * The points on border in this case are not placed twice.
+ */
+void generate_points_grid(Point_Vector& W, int width, int D, bool torus) {
+  int nb_points = 1;
+  for (int i = 0; i < D; ++i)
+    nb_points *= width;
+  for (int i = 0; i < nb_points; ++i) {
+    std::vector<double> point;
+    int cell_i = i;
+    for (int l = 0; l < D; ++l) {
+      if (torus)
+        point.push_back(-1 + (2.0 / (width - 1))*(cell_i % width));
+      else
+        point.push_back(-1 + (2.0 / width)*(cell_i % width));
+      // attention: the bottom and the right are covered too!
+      cell_i /= width;
+    }
+    W.push_back(point);
+  }
+}
+
+/** \brief Generate nbP points uniformly in a cube of side 2
+ * having {+-1}^dim as its vertices and insert them in W.
+ */
+void generate_points_random_box(Point_Vector& W, int nbP, int dim) {
+  Random_cube_iterator rp(dim, 1.0);
+  for (int i = 0; i < nbP; i++) {
+    W.push_back(*rp++);
+  }
+}
+
+/** \brief Generate nbP points uniformly on a (dim-1)-sphere
+ *  and insert them in W.
+ */
+void generate_points_sphere(Point_Vector& W, int nbP, int dim) {
+  CGAL::Random_points_on_sphere_d<Point_d> rp(dim, 1);
+  for (int i = 0; i < nbP; i++)
+    W.push_back(*rp++);
+}
+
+#endif  // EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
new file mode 100644
index 00000000..d94502b1
--- /dev/null
+++ b/src/Witness_complex/example/witness_complex_from_file.cpp
@@ -0,0 +1,116 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2015  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/>.
+ */
+
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Landmark_choice_by_random_point.h>
+#include <gudhi/reader_utils.h>
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <string>
+#include <vector>
+
+using namespace Gudhi;
+using namespace Gudhi::witness_complex;
+
+typedef std::vector< Vertex_handle > typeVectorVertex;
+typedef std::vector< std::vector <double> > Point_Vector;
+
+typedef Witness_complex< Simplex_tree<> > WitnessComplex;
+
+/**
+ * \brief Customized version of read_points
+ * which takes into account a possible nbP first line
+ *
+ */
+inline void
+read_points_cust(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);
+    }
+    if (point.size() != 1)
+      points.push_back(point);
+  }
+  in_file.close();
+}
+
+/** Write a gnuplot readable file.
+ *  Data range is a random access range of pairs (arg, value)
+ */
+template < typename Data_range >
+void write_data(Data_range & data, std::string filename) {
+  std::ofstream ofs(filename, std::ofstream::out);
+  for (auto entry : data)
+    ofs << entry.first << ", " << entry.second << "\n";
+  ofs.close();
+}
+
+int main(int argc, char * const argv[]) {
+  if (argc != 3) {
+    std::cerr << "Usage: " << argv[0]
+        << " path_to_point_file nbL \n";
+    return 0;
+  }
+
+  std::string file_name = argv[1];
+  int nbL = atoi(argv[2]);
+  clock_t start, end;
+
+  // Construct the Simplex Tree
+  Simplex_tree<> simplex_tree;
+
+  // Read the point file
+  Point_Vector point_vector;
+  read_points_cust(file_name, point_vector);
+  std::cout << "Successfully read " << point_vector.size() << " points.\n";
+  std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
+
+  // Choose landmarks
+  start = clock();
+  std::vector<std::vector< int > > knn;
+  Landmark_choice_by_random_point(point_vector, nbL, knn);
+  end = clock();
+  std::cout << "Landmark choice for " << nbL << " landmarks took "
+      << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+
+  // Compute witness complex
+  start = clock();
+  WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+  end = clock();
+  std::cout << "Witness complex took "
+      << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+}
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
new file mode 100644
index 00000000..36f63437
--- /dev/null
+++ b/src/Witness_complex/example/witness_complex_sphere.cpp
@@ -0,0 +1,96 @@
+/*    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):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2015  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/>.
+ */
+#define BOOST_PARAMETER_MAX_ARITY 12
+
+
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Landmark_choice_by_random_point.h>
+#include <gudhi/reader_utils.h>
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <utility>
+#include <string>
+#include <vector>
+
+#include "generators.h"
+
+using namespace Gudhi;
+using namespace Gudhi::witness_complex;
+
+typedef std::vector< Vertex_handle > typeVectorVertex;
+
+typedef Witness_complex< Simplex_tree<> > WitnessComplex;
+
+/** Write a gnuplot readable file.
+ *  Data range is a random access range of pairs (arg, value)
+ */
+template < typename Data_range >
+void write_data(Data_range & data, std::string filename) {
+  std::ofstream ofs(filename, std::ofstream::out);
+  for (auto entry : data)
+    ofs << entry.first << ", " << entry.second << "\n";
+  ofs.close();
+}
+
+int main(int argc, char * const argv[]) {
+  if (argc != 2) {
+    std::cerr << "Usage: " << argv[0]
+        << " nbL \n";
+    return 0;
+  }
+
+  int nbL = atoi(argv[1]);
+  clock_t start, end;
+
+  // Construct the Simplex Tree
+  Simplex_tree<> simplex_tree;
+
+  std::vector< std::pair<int, double> > l_time;
+
+  // Read the point file
+  for (int nbP = 500; nbP < 10000; nbP += 500) {
+    Point_Vector point_vector;
+    generate_points_sphere(point_vector, nbP, 4);
+    std::cout << "Successfully generated " << point_vector.size() << " points.\n";
+    std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n";
+
+    // Choose landmarks
+    start = clock();
+    std::vector<std::vector< int > > knn;
+    Landmark_choice_by_random_point(point_vector, nbL, knn);
+
+    // Compute witness complex
+    WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size());
+    end = clock();
+    double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
+    std::cout << "Witness complex for " << nbL << " landmarks took "
+        << time << " s. \n";
+    l_time.push_back(std::make_pair(nbP, time));
+  }
+  write_data(l_time, "w_time.dat");
+}