Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2013 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 28547c36fb65eea6cf30091678e132763c3d0507

11 files changed, 239 insertions, 35 deletions

diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt
index f70dd8ff..355e8d31 100644
--- a/src/Bottleneck_distance/benchmark/CMakeLists.txt
+++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt
@@ -6,8 +6,6 @@ project(Bottleneck_distance_benchmark)
 # cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      add_executable ( bottleneck_chrono bottleneck_chrono.cpp )
-    endif()
+    add_executable ( bottleneck_chrono bottleneck_chrono.cpp )
   endif ()
 endif()
diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h
index 2706716b..b157f22a 100644
--- a/src/Bottleneck_distance/concept/Persistence_diagram.h
+++ b/src/Bottleneck_distance/concept/Persistence_diagram.h
@@ -25,24 +25,25 @@
 
 namespace Gudhi {
 
-namespace bottleneck_distance {
+namespace persistence_diagram {
 
-/** \brief Concept of Diagram_point. std::get<0>(point) must return the birth of the corresponding component and std::get<1>(point) its death.
+/** \brief Concept of point in a persistence diagram. std::get<0>(point) must return the birth of the corresponding component and std::get<1>(point) its death.
+ * Both should be convertible to `double`.
  * A valid implementation of this concept is std::pair<double,double>.
  * Death should be larger than birth, death can be std::numeric_limits<double>::infinity() for components which stay alive.
  *
  * \ingroup bottleneck_distance
  */
-typename Diagram_point;
+struct DiagramPoint{};
 
-/** \brief Concept of persistence diagram. It's a range of Diagram_point.
+/** \brief Concept of persistence diagram. It is a range of `DiagramPoint`.
  * std::begin(diagram) and std::end(diagram) must return corresponding iterators.
  *
  * \ingroup bottleneck_distance
  */
-typename Persistence_Diagram;
+struct PersistenceDiagram{};
 
-}  // namespace bottleneck_distance
+}  // namespace persistence_diagram
 
 }  // namespace Gudhi
 
diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
index 21187f9c..5223678d 100644
--- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
+++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h
@@ -26,7 +26,7 @@
 // needs namespace for Doxygen to link on classes
 namespace Gudhi {
 // needs namespace for Doxygen to link on classes
-namespace bottleneck_distance {
+namespace persistence_diagram {
 
 /**  \defgroup bottleneck_distance Bottleneck distance
  * 
@@ -35,7 +35,7 @@ namespace bottleneck_distance {
  * 
  * \section bottleneckdefinition Definition
  * 
- * The bottleneck distance measures the similarity between two persistence diagrams. It's the shortest distance b for which there exists a perfect matching between
+ * The bottleneck distance measures the similarity between two persistence diagrams. It is the shortest distance b for which there exists a perfect matching between
  * the points of the two diagrams (completed with all the points on the diagonal in order to ignore cardinality mismatchs) such that
  * any couple of matched points are at distance at most b.
  *
@@ -44,7 +44,7 @@ namespace bottleneck_distance {
  */
 /** @} */  // end defgroup bottleneck_distance
 
-}  // namespace bottleneck_distance
+}  // namespace persistence_diagram
 
 }  // namespace Gudhi
 
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index c66623e9..b36d0f34 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -5,11 +5,18 @@ project(Bottleneck_distance_examples)
 # cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
-      add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
+    add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
+    add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
+
+    add_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example)
+
+    add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
+    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+    if (TBB_FOUND)
+      target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
+    endif(TBB_FOUND)
+    add_test(alpha_rips_persistence_bottleneck_distance ${CMAKE_CURRENT_BINARY_DIR}/alpha_rips_persistence_bottleneck_distance
+        ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.15 -m 0.12 -d 3 -p 3)
 
-      add_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example)
-    endif()
   endif ()
 endif()
diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
new file mode 100644
index 00000000..6e9be97b
--- /dev/null
+++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
@@ -0,0 +1,190 @@
+/*    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):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2017  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
+ *    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/Alpha_complex.h>
+#include <gudhi/Rips_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/Bottleneck.h>
+
+#include <CGAL/Epick_d.h>
+
+#include <boost/program_options.hpp>
+
+#include <string>
+#include <vector>
+#include <limits>  // infinity
+#include <utility>  // for pair
+#include <algorithm>  // for transform
+
+
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp >;
+using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+using Point_d = Kernel::Point_d;
+using Points_off_reader = Gudhi::Points_off_reader<Point_d>;
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+static inline std::pair<double, double> compute_root_square (std::pair<double, double> input) {
+  return std::make_pair(std::sqrt(input.first), std::sqrt(input.second));
+}
+
+int main(int argc, char * argv[]) {
+  std::string off_file_points;
+  Filtration_value threshold;
+  int dim_max;
+  int p;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, off_file_points, threshold, dim_max, p, min_persistence);
+
+  Points_off_reader off_reader(off_file_points);
+
+  // --------------------------------------------
+  // Rips persistence
+  // --------------------------------------------
+  Rips_complex rips_complex(off_reader.get_point_cloud(), threshold, Euclidean_distance());
+
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree rips_stree;
+
+  rips_complex.create_complex(rips_stree, dim_max);
+  std::cout << "The Rips complex contains " << rips_stree.num_simplices() << " simplices and has dimension "
+            << rips_stree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  rips_stree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology rips_pcoh(rips_stree);
+  // initializes the coefficient field for homology
+  rips_pcoh.init_coefficients(p);
+  rips_pcoh.compute_persistent_cohomology(min_persistence);
+
+  // rips_pcoh.output_diagram();
+
+  // --------------------------------------------
+  // Alpha persistence
+  // --------------------------------------------
+  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex(off_reader.get_point_cloud());
+
+  Simplex_tree alpha_stree;
+  alpha_complex.create_complex(alpha_stree, threshold * threshold);
+  std::cout << "The Alpha complex contains " << alpha_stree.num_simplices() << " simplices and has dimension "
+            << alpha_stree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  alpha_stree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology alpha_pcoh(alpha_stree);
+  // initializes the coefficient field for homology
+  alpha_pcoh.init_coefficients(p);
+  alpha_pcoh.compute_persistent_cohomology(min_persistence * min_persistence);
+
+  // alpha_pcoh.output_diagram();
+
+  // --------------------------------------------
+  // Bottleneck distance between both persistence
+  // --------------------------------------------
+  double max_b_distance {};
+  for (int dim = 0; dim < dim_max; dim ++) {
+    std::vector< std::pair< Filtration_value , Filtration_value > > rips_intervals;
+    std::vector< std::pair< Filtration_value , Filtration_value > > alpha_intervals;
+    rips_intervals = rips_pcoh.intervals_in_dimension(dim);
+    alpha_intervals = alpha_pcoh.intervals_in_dimension(dim);
+    std::transform(alpha_intervals.begin(), alpha_intervals.end(), alpha_intervals.begin(), compute_root_square);
+
+    double bottleneck_distance = Gudhi::persistence_diagram::bottleneck_distance(rips_intervals, alpha_intervals);
+    std::cout << "In dimension " << dim << ", bottleneck distance = " << bottleneck_distance << std::endl;
+    if (bottleneck_distance > max_b_distance)
+      max_b_distance = bottleneck_distance;
+  }
+  std::cout << "================================================================================" << std::endl;
+  std::cout << "Bottleneck distance is " << max_b_distance << std::endl;
+
+  return 0;
+}
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence) {
+  namespace po = boost::program_options;
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&off_file_points),
+       "Name of an OFF file containing a point set.\n");
+
+  po::options_description visible("Allowed options", 100);
+  visible.add_options()
+      ("help,h", "produce help message")
+      ("max-edge-length,r",
+       po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+       "Maximal length of an edge for the Rips complex construction.")
+      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
+       "Maximal dimension of the Rips complex we want to compute.")
+      ("field-charac,p", po::value<int>(&p)->default_value(11),
+       "Characteristic p of the coefficient field Z/pZ for computing homology.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+
+  po::positional_options_description pos;
+  pos.add("input-file", 1);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
+
+  po::variables_map vm;
+  po::store(po::command_line_parser(argc, argv).
+            options(all).positional(pos).run(), vm);
+  po::notify(vm);
+
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of a Rips complex defined on a set of input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}
diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
index b5641e29..b90a0ee0 100644
--- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h
+++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
@@ -80,11 +80,22 @@ double bottleneck_distance_exact(Persistence_graph& g) {
   return sd.at(lower_bound_i);
 }
 
-/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams (see concepts).
- * If the last parameter e is not 0, you get an additive e-approximation, which is a lot faster to compute whatever is
- * e.
- * Thus, by default, e is a very small positive double, actually the smallest double possible such that the
- * floating-point inaccuracies don't lead to a failure of the algorithm.
+/** \brief Function to compute the Bottleneck distance between two persistence diagrams.
+ *
+ * \tparam Persistence_diagram1,Persistence_diagram2
+ * models of the concept `PersistenceDiagram`.
+ * \param[in] e
+ * \parblock
+ * If `e` is 0, this uses an expensive algorithm to compute the exact distance.
+ *
+ * If `e` is not 0, it asks for an additive `e`-approximation, and currently
+ * also allows a small multiplicative error (the last 2 or 3 bits of the
+ * mantissa may be wrong). This version of the algorithm takes advantage of the
+ * limited precision of `double` and is usually a lot faster to compute,
+ * whatever the value of `e`.
+ *
+ * Thus, by default, `e` is the smallest positive double.
+ * \endparblock
  *
  * \ingroup bottleneck_distance
  */
diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
index 39efc082..c7695112 100644
--- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
+++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
@@ -40,7 +40,7 @@ namespace persistence_diagram {
  */
 class Persistence_graph {
  public:
-  /** \internal \brief Constructor taking 2 Persistence_Diagrams (concept) as parameters. */
+  /** \internal \brief Constructor taking 2 PersistenceDiagrams (concept) as parameters. */
   template<typename Persistence_diagram1, typename Persistence_diagram2>
   Persistence_graph(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e);
   /** \internal \brief Is the given point from U the projection of a point in V ? */
diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt
index a6979d3c..6c8f112d 100644
--- a/src/Bottleneck_distance/test/CMakeLists.txt
+++ b/src/Bottleneck_distance/test/CMakeLists.txt
@@ -15,14 +15,12 @@ endif()
 # cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      add_executable ( bottleneckUT bottleneck_unit_test.cpp )
-      target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+    add_executable ( bottleneckUT bottleneck_unit_test.cpp )
+    target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-      # Unitary tests
-      add_test(NAME bottleneckUT COMMAND ${CMAKE_CURRENT_BINARY_DIR}/bottleneckUT
-        # XML format for Jenkins xUnit plugin 
-        --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/bottleneckUT.xml --log_level=test_suite --report_level=no)
-    endif()
+    # Unitary tests
+    add_test(NAME bottleneckUT COMMAND ${CMAKE_CURRENT_BINARY_DIR}/bottleneckUT
+      # XML format for Jenkins xUnit plugin
+      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/bottleneckUT.xml --log_level=test_suite --report_level=no)
   endif ()
 endif()
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index ca5a919c..60c9cd07 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -293,10 +293,6 @@ make \endverbatim
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
  * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="_bottleneck_distance_2_bottleneck_basic_example_8cpp-example.html">
- * Bottleneck_distance/bottleneck_basic_example.cpp</a>
- * \li <a href="_bottleneck_distance_2_bottleneck_read_file_example_8cpp-example.html">
- * Bottleneck_distance/bottleneck_read_file_example.cpp</a>
  * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
  * Persistent_cohomology/alpha_complex_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 998908e7..6c49c800 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -75,10 +75,12 @@ if(PYTHON_PATH AND CYTHON_PATH)
     
         set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'")
         set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'")
+        set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'")
       else (NOT CGAL_VERSION VERSION_LESS 4.8.0)
         # Remove alpha complex unitary tests
         file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_alpha_complex.py)
         file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py)
+        file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py)
       endif (NOT CGAL_VERSION VERSION_LESS 4.8.0)
     endif (CGAL_FOUND)
     
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index 5dcb9d48..2d743d4d 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -33,3 +33,4 @@ include "cython/witness_complex.pyx"
 @GUDHI_CYTHON_ALPHA_COMPLEX@
 @GUDHI_CYTHON_SUBSAMPLING@
 @GUDHI_CYTHON_TANGENTIAL_COMPLEX@
+@GUDHI_CYTHON_BOTTLENECK_DISTANCE@