Add distance matrix rips construction (doc, code, test)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1766 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 6b9bdecbaf0aca12facb023e66bdea71e8e8cd38

5 files changed, 62 insertions, 54 deletions

diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 85310f66..85ae8679 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -60,7 +60,7 @@
 <table border="0">
   <tr>
     <td width="25%">
-      <b>Author:</b> Cl&eacute;ment Maria<br>
+      <b>Author:</b> Cl&eacute;ment Maria, Pawel Dlotko, Vincent Rouvreau<br>
       <b>Introduced in:</b> GUDHI 1.4.0<br>
       <b>Copyright:</b> GPL v3<br>
     </td>
@@ -68,6 +68,7 @@
     Rips_complex is a simplicial complex constructed from a one skeleton graph.<br>
     The filtration value of each edge is computed from a user-given distance function and is inserted until a
     user-given threshold value.<br>
+    This complex can be built from a point cloud and a distance function, or from a distance matrix.<br>
     <b>User manual:</b> \ref rips_complex - <b>Reference manual:</b> Gudhi::rips_complex::Rips_complex
     </td>
  </tr>
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index 006df275..ed2c1f5d 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
@@ -25,9 +25,12 @@
 
 #include <cmath>  // for std::sqrt
 
-/* Compute the Euclidean distance between two Points given
- * by a range of coordinates. The points are assumed to have 
- * the same dimension. */
+/** @file
+ * @brief Global distance functions
+ */
+
+/** @brief Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to
+ * have the same dimension. */
 template< typename Filtration_value, typename Point >
 Filtration_value euclidean_distance(const Point &p1,const Point &p2) {
   Filtration_value dist = 0.;
diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h
index 9dbcd891..5fe7c826 100644
--- a/src/common/include/gudhi/graph_simplicial_complex.h
+++ b/src/common/include/gudhi/graph_simplicial_complex.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Clément Maria
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *    Copyright (C) 2014  INRIA
  *
  *    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
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 40d566d8..3799e583 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -34,14 +34,20 @@
 #include <string>
 #include <vector>
 
+// Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented.
+// It is required for global functions and variables.
+
+/** @file
+ * @brief This file includes common file reader for GUDHI
+ */
+
 /**
- * \brief Read a set of points to turn it
- * into a vector< vector<double> > by filling points
+ * @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
+ * File format: 1 point per line<br>
+ * X11 X12 ... X1d<br>
+ * X21 X22 ... X2d<br>
+ * etc<br>
  */
 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);
@@ -66,12 +72,12 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
 }
 
 /**
- * \brief Read a graph from a file.
+ * @brief Read a graph from a file.
  *
- * File format: 1 simplex per line
- * Dim1 X11 X12 ... X1d Fil1 
- * Dim2 X21 X22 ... X2d Fil2
- * etc
+ * File format: 1 simplex per line<br>
+ * Dim1 X11 X12 ... X1d Fil1<br>
+ * Dim2 X21 X22 ... X2d Fil2<br>
+ * etc<br>
  *
  * The vertices must be labeled from 0 to n-1.
  * Every simplex must appear exactly once.
@@ -141,12 +147,12 @@ inline Graph_t read_graph(std::string file_name) {
 }
 
 /**
- * \brief Read a face from a file.
+ * @brief Read a face from a file.
  *
- * File format: 1 simplex per line
- * Dim1 X11 X12 ... X1d Fil1 
- * Dim2 X21 X22 ... X2d Fil2
- * etc
+ * File format: 1 simplex per line<br>
+ * Dim1 X11 X12 ... X1d Fil1<br>
+ * Dim2 X21 X22 ... X2d Fil2<br>
+ * etc<br>
  *
  * The vertices must be labeled from 0 to n-1.
  * Every simplex must appear exactly once.
@@ -167,18 +173,16 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi
 }
 
 /**
- * \brief Read a hasse simplex from a file.
+ * @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
+ * File format: 1 simplex per line<br>
+ * Dim1 k11 k12 ... k1Dim1 Fil1<br>
+ * Dim2 k21 k22 ... k2Dim2 Fil2<br>
+ * etc<br>
  *
- * 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.*/
+ * 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;
@@ -197,27 +201,27 @@ 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
+ * @brief Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole
  * (square) matrix.
  * 
- * \author Pawel Dlotko
+ * @author Pawel Dlotko
  *
- * Square matrix file format:
- * 0;D12;...;D1j
- * D21;0;...;D2j
- * ...
- * Dj1;Dj2;...;0
+ * Square matrix file format:<br>
+ * 0;D12;...;D1j<br>
+ * D21;0;...;D2j<br>
+ * ...<br>
+ * Dj1;Dj2;...;0<br>
  *
- * lower matrix file format:
- * 0
- * D21;
- * D31;D32;
- * ...
- * Dj1;Dj2;...;Dj(j-1);
+ * lower matrix file format:<br>
+ * 0<br>
+ * D21;<br>
+ * D31;D32;<br>
+ * ...<br>
+ * Dj1;Dj2;...;Dj(j-1);<br>
  *
  **/
 template< typename Filtration_value >
-std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(std::string filename,
+std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string& filename,
                                                                                           const char separator=';') {
   bool dbg = false;
   if (dbg) {
diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp
index 7eb7e846..a4c46bb1 100644
--- a/src/common/test/test_distance_matrix_reader.cpp
+++ b/src/common/test/test_distance_matrix_reader.cpp
@@ -47,21 +47,21 @@ BOOST_AUTO_TEST_CASE( lower_triangular_distance_matrix )
   std::cout << "from_lower_triangular size = " << from_lower_triangular.size() << std::endl;
   BOOST_CHECK(from_lower_triangular.size() == 5);
 
-  for (int i = 0; i < from_lower_triangular.size(); i++) {
+  for (std::size_t i = 0; i < from_lower_triangular.size(); i++) {
     std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl;
     BOOST_CHECK(from_lower_triangular[i].size() == i);
   }
   std::vector<double> expected = {1};
-  BOOST_CHECK(from_lower_triangular[0] == expected);
+  BOOST_CHECK(from_lower_triangular[1] == expected);
   
   expected = {2,3};
-  BOOST_CHECK(from_lower_triangular[0] == expected);
+  BOOST_CHECK(from_lower_triangular[2] == expected);
   
   expected = {4,5,6};
-  BOOST_CHECK(from_lower_triangular[0] == expected);
+  BOOST_CHECK(from_lower_triangular[3] == expected);
   
   expected = {7,8,9,10};
-  BOOST_CHECK(from_lower_triangular[0] == expected);
+  BOOST_CHECK(from_lower_triangular[4] == expected);
   
 }
 
@@ -78,8 +78,8 @@ BOOST_AUTO_TEST_CASE( full_square_distance_matrix )
   }
   std::cout << "from_full_square size = " << from_full_square.size() << std::endl;
   BOOST_CHECK(from_full_square.size() == 5);
-  for (int i = 0; i < from_lower_triangular.size(); i++) {
-    std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl;
-    BOOST_CHECK(from_lower_triangular[i].size() == i);
+  for (std::size_t i = 0; i < from_full_square.size(); i++) {
+    std::cout << "from_full_square[" << i << "] size = " << from_full_square[i].size() << std::endl;
+    BOOST_CHECK(from_full_square[i].size() == i);
   }  
 }