Code review : fix camel case for types and use of std::log instead of log

Add CGAL dependency for Nerve_GIC (link to bottleneck)
Add persistence representation in bibtex


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3155 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 8a45497b3d1f34a5c4a1c7856113c6b7680a12a2

5 files changed, 61 insertions, 45 deletions

diff --git a/biblio/how_to_cite_gudhi.bib b/biblio/how_to_cite_gudhi.bib
index 28014ade..5994124a 100644
--- a/biblio/how_to_cite_gudhi.bib
+++ b/biblio/how_to_cite_gudhi.bib
@@ -128,6 +128,15 @@
 , title =   "Cover complex"
 , publisher =  "{GUDHI Editorial Board}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "http://gudhi.gforge.inria.fr/doc/latest/group__bottleneck__distance.html"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__cover__complex.html"
+, year =        2017
+}
+
+@incollection{gudhi:PersistenceRepresentations
+, author =  "Pawel Dlotko"
+, title =   "Persistence representations"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group___persistence__representations.html"
 , year =        2017
 }
diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt
index 461b6db2..73728dc0 100644
--- a/src/Nerve_GIC/example/CMakeLists.txt
+++ b/src/Nerve_GIC/example/CMakeLists.txt
@@ -1,29 +1,33 @@
 cmake_minimum_required(VERSION 2.6)
 project(Nerve_GIC_examples)
 
-add_executable ( Nerve Nerve.cpp )
-add_executable ( CoordGIC CoordGIC.cpp )
-add_executable ( FuncGIC FuncGIC.cpp )
-add_executable ( VoronoiGIC VoronoiGIC.cpp )
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
-if (TBB_FOUND)
-  target_link_libraries(Nerve ${TBB_LIBRARIES})
-  target_link_libraries(CoordGIC ${TBB_LIBRARIES})
-  target_link_libraries(FuncGIC ${TBB_LIBRARIES})
-  target_link_libraries(VoronoiGIC ${TBB_LIBRARIES})
-endif()
+  add_executable ( Nerve Nerve.cpp )
+  add_executable ( CoordGIC CoordGIC.cpp )
+  add_executable ( FuncGIC FuncGIC.cpp )
+  add_executable ( VoronoiGIC VoronoiGIC.cpp )
 
-file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  if (TBB_FOUND)
+    target_link_libraries(Nerve ${TBB_LIBRARIES})
+    target_link_libraries(CoordGIC ${TBB_LIBRARIES})
+    target_link_libraries(FuncGIC ${TBB_LIBRARIES})
+    target_link_libraries(VoronoiGIC ${TBB_LIBRARIES})
+  endif()
 
-add_test(NAME Nerve_GIC_example_nerve COMMAND $<TARGET_FILE:Nerve>
-    "${CMAKE_SOURCE_DIR}/data/points/human.off" "2" "10" "0.3")
+  file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-add_test(NAME Nerve_GIC_example_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC>
-    "${CMAKE_SOURCE_DIR}/data/points/human.off" "100")
+  add_test(NAME Nerve_GIC_example_nerve COMMAND $<TARGET_FILE:Nerve>
+      "${CMAKE_SOURCE_DIR}/data/points/human.off" "2" "10" "0.3")
 
-add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC>
-    "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0")
+  add_test(NAME Nerve_GIC_example_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC>
+      "${CMAKE_SOURCE_DIR}/data/points/human.off" "100")
 
-add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC>
-    "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off"
-    "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1")
+  add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0")
+
+  add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC>
+      "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off"
+      "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1")
+
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h
index 2fd61f14..27030723 100644
--- a/src/Nerve_GIC/include/gudhi/GIC.h
+++ b/src/Nerve_GIC/include/gudhi/GIC.h
@@ -58,13 +58,13 @@ namespace cover_complex {
 using Simplex_tree = Gudhi::Simplex_tree<>;
 using Filtration_value = Simplex_tree::Filtration_value;
 using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
-using PersistenceDiagram = std::vector<std::pair<double, double> >;
+using Persistence_diagram = std::vector<std::pair<double, double> >;
 using Graph = boost::subgraph<
     boost::adjacency_list<boost::setS, boost::vecS, boost::undirectedS, boost::no_property,
                           boost::property<boost::edge_index_t, int, boost::property<boost::edge_weight_t, double> > > >;
-using vertex_t = boost::graph_traits<Graph>::vertex_descriptor;
-using IndexMap = boost::property_map<Graph, boost::vertex_index_t>::type;
-using WeightMap = boost::property_map<Graph, boost::edge_weight_t>::type;
+using Vertex_t = boost::graph_traits<Graph>::vertex_descriptor;
+using Index_map = boost::property_map<Graph, boost::vertex_index_t>::type;
+using Weight_map = boost::property_map<Graph, boost::edge_weight_t>::type;
 
 /**
  * \class Cover_complex
@@ -105,12 +105,12 @@ class Cover_complex {
 
   Graph one_skeleton_OFF;          // one-skeleton given by the input OFF file (if it exists).
   Graph one_skeleton;              // one-skeleton used to compute the connected components.
-  std::vector<vertex_t> vertices;  // vertices of one_skeleton.
+  std::vector<Vertex_t> vertices;  // vertices of one_skeleton.
 
   std::vector<std::vector<int> > simplices;  // simplices of output simplicial complex.
   std::vector<int> voronoi_subsamples;       // Voronoi germs (in case of Voronoi cover).
 
-  PersistenceDiagram PD;
+  Persistence_diagram PD;
   std::vector<double> distribution;
 
   std::map<int, std::vector<int> >
@@ -359,8 +359,8 @@ class Cover_complex {
 
  public:
   void set_graph_weights() {
-    IndexMap index = boost::get(boost::vertex_index, one_skeleton);
-    WeightMap weight = boost::get(boost::edge_weight, one_skeleton);
+    Index_map index = boost::get(boost::vertex_index, one_skeleton);
+    Weight_map weight = boost::get(boost::edge_weight, one_skeleton);
     boost::graph_traits<Graph>::edge_iterator ei, ei_end;
     for (boost::tie(ei, ei_end) = boost::edges(one_skeleton); ei != ei_end; ++ei)
       boost::put(weight, *ei,
@@ -420,7 +420,7 @@ class Cover_complex {
    */
   template <typename Distance>
   double set_graph_from_automatic_rips(Distance distance, int N = 100) {
-    int m = floor(n / exp((1 + rate_power) * log(log(n) / log(rate_constant))));
+    int m = floor(n / std::exp((1 + rate_power) * std::log(std::log(n) / std::log(rate_constant))));
     m = std::min(m, n - 1);
     std::vector<int> samples(m);
     double delta = 0;
@@ -521,7 +521,7 @@ class Cover_complex {
     }
 
     double reso = 0;
-    IndexMap index = boost::get(boost::vertex_index, one_skeleton);
+    Index_map index = boost::get(boost::vertex_index, one_skeleton);
 
     if (type == "GIC") {
       boost::graph_traits<Graph>::edge_iterator ei, ei_end;
@@ -660,7 +660,7 @@ class Cover_complex {
 
     int id = 0;
     int pos = 0;
-    IndexMap index = boost::get(boost::vertex_index, one_skeleton);  // int maxc = -1;
+    Index_map index = boost::get(boost::vertex_index, one_skeleton);  // int maxc = -1;
     std::map<int, std::vector<int> > preimages;
     std::map<int, double> funcstd;
 
@@ -799,8 +799,8 @@ class Cover_complex {
     SampleWithoutReplacement(n, m, voronoi_subsamples);
     if (distances.size() == 0) compute_pairwise_distances(distance);
     set_graph_weights();
-    WeightMap weight = boost::get(boost::edge_weight, one_skeleton);
-    IndexMap index = boost::get(boost::vertex_index, one_skeleton);
+    Weight_map weight = boost::get(boost::edge_weight, one_skeleton);
+    Index_map index = boost::get(boost::vertex_index, one_skeleton);
     std::vector<double> mindist(n);
     for (int j = 0; j < n; j++) mindist[j] = std::numeric_limits<double>::max();
 
@@ -1220,7 +1220,7 @@ class Cover_complex {
     }
 
     if (type == "GIC") {
-      IndexMap index = boost::get(boost::vertex_index, one_skeleton);
+      Index_map index = boost::get(boost::vertex_index, one_skeleton);
 
       if (functional_cover) {
         // Computes the simplices in the GIC by looking at all the edges of the graph and adding the
diff --git a/src/Nerve_GIC/test/CMakeLists.txt b/src/Nerve_GIC/test/CMakeLists.txt
index 03fe47ca..c35cdff7 100644
--- a/src/Nerve_GIC/test/CMakeLists.txt
+++ b/src/Nerve_GIC/test/CMakeLists.txt
@@ -1,14 +1,17 @@
 cmake_minimum_required(VERSION 2.6)
 project(Graph_induced_complex_tests)
 
-include(GUDHI_test_coverage)
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+  include(GUDHI_test_coverage)
 
-add_executable ( Nerve_GIC_test_unit test_GIC.cpp )
-target_link_libraries(Nerve_GIC_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-if (TBB_FOUND)
-  target_link_libraries(Nerve_GIC_test_unit ${TBB_LIBRARIES})
-endif()
+  add_executable ( Nerve_GIC_test_unit test_GIC.cpp )
+  target_link_libraries(Nerve_GIC_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Nerve_GIC_test_unit ${TBB_LIBRARIES})
+  endif()
 
-file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-gudhi_add_coverage_test(Nerve_GIC_test_unit)
+  gudhi_add_coverage_test(Nerve_GIC_test_unit)
+
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Nerve_GIC/test/test_GIC.cpp b/src/Nerve_GIC/test/test_GIC.cpp
index a8b1e7f7..d633753c 100644
--- a/src/Nerve_GIC/test/test_GIC.cpp
+++ b/src/Nerve_GIC/test/test_GIC.cpp
@@ -24,11 +24,11 @@
 #define BOOST_TEST_MODULE "graph_induced_complex"
 
 #include <boost/test/unit_test.hpp>
-#include <cmath>  // float comparison
+
 #include <limits>
 #include <string>
 #include <vector>
-#include <algorithm>  // std::max
+
 #include <gudhi/GIC.h>
 #include <gudhi/distance_functions.h>
 #include <gudhi/reader_utils.h>